Starting phenix.real_space_refine on Thu May 29 00:37:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxq_43629/05_2025/8vxq_43629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxq_43629/05_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_43629/05_2025/8vxq_43629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxq_43629/05_2025/8vxq_43629.map" model { file = "/net/cci-nas-00/data/ceres_data/8vxq_43629/05_2025/8vxq_43629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxq_43629/05_2025/8vxq_43629.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 17.25, per 1000 atoms: 0.55 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: 7.80 Conformation dependent library (CDL) restraints added in 4.4 seconds 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: 2.72 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: 9.66 Time building geometry restraints manager: 9.02 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: 0.02 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: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.100 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 64.050 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.750 ------------------------------------------------------------------------------- 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 : 3.22 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (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 TRP 0.015 0.002 TRP A 77 HIS 0.004 0.001 HIS R 198 PHE 0.044 0.002 PHE O 211 TYR 0.044 0.001 TYR B 116 ARG 0.016 0.001 ARG J 223 Details of bonding type rmsd hydrogen bonds : bond 0.11242 ( 2290) hydrogen bonds : angle 4.61250 ( 6843) covalent geometry : bond 0.00405 (31860) covalent geometry : angle 0.70849 (42867) *********************** 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 : 3.295 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: 0.4288 time to fit residues: 290.5702 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 : 3.512 ------------------------------------------------------------------------------- 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 341 optimal weight: 2.9990 chunk 306 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 207 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 317 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 193 optimal weight: 0.2980 chunk 236 optimal weight: 0.0020 chunk 367 optimal weight: 0.0050 overall best weight: 0.3202 ------------------------------------------------------------------------------- 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 M 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.214257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122786 restraints weight = 49195.929| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.89 r_work: 0.3191 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31860 Z= 0.131 Angle : 0.510 6.615 42867 Z= 0.272 Chirality : 0.034 0.155 4635 Planarity : 0.004 0.170 5985 Dihedral : 3.585 48.859 4588 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.03 % Rotamer: Outliers : 2.02 % Allowed : 27.93 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.14), residues: 4122 helix: 3.04 (0.10), residues: 2979 sheet: None (None), residues: 0 loop : -3.16 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 77 HIS 0.002 0.001 HIS R 198 PHE 0.030 0.001 PHE B 112 TYR 0.022 0.001 TYR B 116 ARG 0.007 0.000 ARG Q 216 Details of bonding type rmsd hydrogen bonds : bond 0.05974 ( 2290) hydrogen bonds : angle 3.56878 ( 6843) covalent geometry : bond 0.00243 (31860) covalent geometry : angle 0.50998 (42867) *********************** 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 508 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 443 time to evaluate : 3.657 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 72 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8428 (tm-30) REVERT: K 42 ARG cc_start: 0.7759 (mtt-85) cc_final: 0.7510 (mtm-85) REVERT: L 90 MET cc_start: 0.9051 (mtp) cc_final: 0.8811 (mtp) REVERT: L 95 ASP cc_start: 0.8742 (t70) cc_final: 0.8224 (t70) REVERT: M 126 GLU cc_start: 0.8875 (tt0) cc_final: 0.8580 (tm-30) REVERT: O 221 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.7886 (ttm110) REVERT: P 42 ARG cc_start: 0.8443 (mmm-85) cc_final: 0.8219 (mmm-85) REVERT: P 215 GLN cc_start: 0.8498 (tt0) cc_final: 0.8244 (tt0) REVERT: Q 42 ARG cc_start: 0.8034 (mtt90) cc_final: 0.7809 (mtm-85) REVERT: Q 101 ASP cc_start: 0.8497 (p0) cc_final: 0.8060 (p0) REVERT: Q 126 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7806 (tm-30) REVERT: Q 185 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8023 (tm-30) REVERT: Q 260 MET cc_start: -0.2544 (mmp) cc_final: -0.3316 (tmm) REVERT: A 63 MET cc_start: 0.6779 (mpt) cc_final: 0.6430 (mpt) REVERT: B 99 ARG cc_start: 0.7054 (mmm-85) cc_final: 0.6553 (tpp-160) REVERT: B 148 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7426 (m-80) REVERT: C 33 MET cc_start: 0.1043 (ttp) cc_final: 0.0483 (ttp) REVERT: C 132 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7394 (mmm160) REVERT: D 51 MET cc_start: 0.1744 (mmm) cc_final: 0.1361 (tpp) REVERT: E 98 GLN cc_start: 0.8402 (tt0) cc_final: 0.8184 (tp40) REVERT: F 98 GLN cc_start: 0.7937 (tt0) cc_final: 0.7601 (tp40) REVERT: F 99 ARG cc_start: 0.7420 (mmm-85) cc_final: 0.6894 (ttt-90) REVERT: F 102 ARG cc_start: 0.8292 (ttm170) cc_final: 0.7968 (ttp-110) REVERT: F 132 ARG cc_start: 0.8089 (tpt90) cc_final: 0.7692 (mmp80) REVERT: H 111 GLN cc_start: 0.8814 (tp40) cc_final: 0.8499 (tp40) REVERT: H 149 MET cc_start: 0.8002 (ttp) cc_final: 0.7679 (ptt) outliers start: 65 outliers final: 29 residues processed: 485 average time/residue: 0.4265 time to fit residues: 323.4949 Evaluate side-chains 446 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 415 time to evaluate : 3.163 ------------------------------------------------------------------------------- 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 94 LEU Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 307 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 238 GLN Chi-restraints excluded: chain M residue 202 MET Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 238 GLN Chi-restraints excluded: chain P residue 228 LEU Chi-restraints excluded: chain P residue 238 GLN Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain A residue 67 VAL 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 C residue 132 ARG 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 H residue 103 ASP Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 103 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 117 optimal weight: 10.0000 chunk 365 optimal weight: 8.9990 chunk 217 optimal weight: 1.9990 chunk 399 optimal weight: 8.9990 chunk 235 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 300 optimal weight: 30.0000 chunk 360 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 95 optimal weight: 0.8980 chunk 303 optimal weight: 0.0370 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 149 ASN J 159 ASN K 156 GLN L 30 GLN M 171 GLN Q 58 ASN A 121 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN D 121 GLN ** D 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN ** F 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.205673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.110137 restraints weight = 49540.995| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.95 r_work: 0.2997 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 31860 Z= 0.284 Angle : 0.627 8.945 42867 Z= 0.340 Chirality : 0.039 0.166 4635 Planarity : 0.004 0.132 5985 Dihedral : 3.969 51.573 4587 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.77 % Favored : 93.04 % Rotamer: Outliers : 3.94 % Allowed : 27.22 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.14), residues: 4122 helix: 2.71 (0.10), residues: 2979 sheet: None (None), residues: 0 loop : -3.25 (0.15), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP A 77 HIS 0.002 0.001 HIS J 198 PHE 0.035 0.002 PHE A 112 TYR 0.017 0.001 TYR G 116 ARG 0.008 0.001 ARG L 216 Details of bonding type rmsd hydrogen bonds : bond 0.07774 ( 2290) hydrogen bonds : angle 3.93630 ( 6843) covalent geometry : bond 0.00650 (31860) covalent geometry : angle 0.62702 (42867) *********************** 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 553 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 426 time to evaluate : 3.977 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: R 101 ASP cc_start: 0.8948 (p0) cc_final: 0.8738 (p0) REVERT: R 107 ILE cc_start: 0.8519 (pt) cc_final: 0.8295 (mt) REVERT: R 260 MET cc_start: -0.0912 (mmp) cc_final: -0.1623 (mmp) REVERT: J 90 MET cc_start: 0.9336 (ttm) cc_final: 0.9081 (ttm) REVERT: J 126 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8295 (tm-30) REVERT: J 217 ASP cc_start: 0.8733 (t0) cc_final: 0.8153 (t0) REVERT: J 220 ARG cc_start: 0.8180 (ttm110) cc_final: 0.7786 (ttp80) REVERT: K 202 MET cc_start: 0.8656 (mmm) cc_final: 0.8381 (mmm) REVERT: L 90 MET cc_start: 0.9394 (mtp) cc_final: 0.9019 (mtp) REVERT: M 42 ARG cc_start: 0.8587 (ptm160) cc_final: 0.7780 (ptp-170) REVERT: N 101 ASP cc_start: 0.8922 (p0) cc_final: 0.8447 (p0) REVERT: O 176 ASN cc_start: 0.8616 (t0) cc_final: 0.8324 (m110) REVERT: O 221 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.8151 (ttm110) REVERT: P 101 ASP cc_start: 0.8899 (p0) cc_final: 0.8612 (p0) REVERT: P 215 GLN cc_start: 0.8668 (tt0) cc_final: 0.8292 (tt0) REVERT: Q 56 GLU cc_start: 0.8918 (tp30) cc_final: 0.8650 (tp30) REVERT: Q 58 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8434 (t160) REVERT: Q 185 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8086 (tm-30) REVERT: Q 221 ARG cc_start: 0.8306 (ttm110) cc_final: 0.7789 (ttm110) REVERT: Q 260 MET cc_start: -0.2589 (mmp) cc_final: -0.3319 (tmm) REVERT: A 3 TYR cc_start: 0.0913 (OUTLIER) cc_final: -0.0012 (p90) REVERT: B 99 ARG cc_start: 0.7245 (mmm-85) cc_final: 0.6713 (tpp-160) REVERT: B 110 ARG cc_start: 0.7014 (ttt-90) cc_final: 0.6649 (ttp80) REVERT: B 148 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: C 1 MET cc_start: 0.3824 (pmm) cc_final: 0.1492 (tpt) REVERT: C 8 MET cc_start: 0.1133 (mmm) cc_final: 0.0747 (mtm) REVERT: C 33 MET cc_start: 0.1125 (ttp) cc_final: 0.0638 (ttp) REVERT: C 51 MET cc_start: 0.2986 (mmp) cc_final: 0.1302 (mtt) REVERT: D 51 MET cc_start: 0.1700 (mmm) cc_final: 0.1381 (tpp) REVERT: D 121 GLN cc_start: 0.7974 (tt0) cc_final: 0.7742 (tm-30) REVERT: E 98 GLN cc_start: 0.8384 (tt0) cc_final: 0.8175 (tp40) REVERT: F 98 GLN cc_start: 0.7948 (tt0) cc_final: 0.7738 (tp40) REVERT: F 99 ARG cc_start: 0.7510 (mmm-85) cc_final: 0.6708 (ttt-90) REVERT: F 114 MET cc_start: 0.8652 (tmm) cc_final: 0.8405 (tmm) REVERT: F 132 ARG cc_start: 0.8133 (tpt90) cc_final: 0.7627 (mmp80) REVERT: F 149 MET cc_start: 0.8894 (tpt) cc_final: 0.8219 (ptt) REVERT: H 77 TRP cc_start: 0.7855 (p90) cc_final: 0.7559 (p90) outliers start: 127 outliers final: 74 residues processed: 521 average time/residue: 0.4496 time to fit residues: 363.5290 Evaluate side-chains 499 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 422 time to evaluate : 3.310 ------------------------------------------------------------------------------- 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 162 GLU 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 170 VAL Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 157 LEU 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 46 MET Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 222 ASP 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 140 SER Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 215 GLN Chi-restraints excluded: chain P residue 93 ASN 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 Q residue 58 ASN Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain Q residue 140 SER 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 148 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 55 SER 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 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 F residue 67 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 67 VAL 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 H residue 111 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 173 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 363 optimal weight: 30.0000 chunk 114 optimal weight: 8.9990 chunk 374 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 404 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 chunk 274 optimal weight: 30.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 30 GLN ** J 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 176 ASN J 247 GLN K 30 GLN K 176 ASN ** K 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 GLN M 176 ASN N 30 GLN N 171 GLN N 176 ASN O 30 GLN P 30 GLN ** P 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 GLN Q 58 ASN Q 322 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN F 111 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.202356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107147 restraints weight = 49387.550| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.78 r_work: 0.2944 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 31860 Z= 0.396 Angle : 0.719 10.629 42867 Z= 0.391 Chirality : 0.043 0.185 4635 Planarity : 0.005 0.133 5985 Dihedral : 4.281 51.443 4585 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.96 % Favored : 92.82 % Rotamer: Outliers : 5.46 % Allowed : 27.31 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.14), residues: 4122 helix: 2.40 (0.10), residues: 2943 sheet: None (None), residues: 0 loop : -3.28 (0.15), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.005 TRP E 77 HIS 0.004 0.002 HIS P 198 PHE 0.051 0.002 PHE O 211 TYR 0.019 0.002 TYR D 142 ARG 0.008 0.001 ARG K 80 Details of bonding type rmsd hydrogen bonds : bond 0.08440 ( 2290) hydrogen bonds : angle 4.18019 ( 6843) covalent geometry : bond 0.00907 (31860) covalent geometry : angle 0.71860 (42867) *********************** 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 605 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 429 time to evaluate : 3.237 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 260 MET cc_start: -0.0161 (mmp) cc_final: -0.0795 (mmp) REVERT: J 220 ARG cc_start: 0.8319 (ttm110) cc_final: 0.7897 (ttp80) REVERT: K 36 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7631 (tt) REVERT: K 202 MET cc_start: 0.8661 (mmm) cc_final: 0.8375 (mmm) REVERT: L 90 MET cc_start: 0.9431 (mtp) cc_final: 0.9065 (mtp) REVERT: L 221 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7982 (ttm110) REVERT: L 260 MET cc_start: 0.1288 (mmp) cc_final: -0.1472 (tmm) REVERT: N 46 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7988 (ttt) REVERT: O 36 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7364 (tt) REVERT: O 95 ASP cc_start: 0.9175 (t0) cc_final: 0.8967 (t0) REVERT: O 176 ASN cc_start: 0.8616 (t0) cc_final: 0.8277 (m-40) REVERT: O 221 ARG cc_start: 0.8686 (ttm-80) cc_final: 0.8460 (ttm110) REVERT: P 42 ARG cc_start: 0.8617 (mmm-85) cc_final: 0.8364 (mmm-85) REVERT: P 101 ASP cc_start: 0.8923 (p0) cc_final: 0.8669 (p0) REVERT: P 135 GLN cc_start: 0.8613 (tt0) cc_final: 0.8264 (tp40) REVERT: P 188 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8055 (mm-40) REVERT: P 215 GLN cc_start: 0.8770 (tt0) cc_final: 0.8396 (tt0) REVERT: Q 42 ARG cc_start: 0.8374 (mtt90) cc_final: 0.7955 (mpt-90) REVERT: Q 56 GLU cc_start: 0.8873 (tp30) cc_final: 0.8566 (tp30) REVERT: Q 101 ASP cc_start: 0.8886 (p0) cc_final: 0.8666 (p0) REVERT: Q 185 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8115 (tm-30) REVERT: Q 260 MET cc_start: -0.2366 (mmp) cc_final: -0.3066 (tmm) REVERT: A 3 TYR cc_start: 0.0928 (OUTLIER) cc_final: -0.0170 (p90) REVERT: B 35 MET cc_start: 0.0045 (OUTLIER) cc_final: -0.1027 (tmm) REVERT: B 104 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7614 (tm-30) REVERT: B 111 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7944 (tm-30) REVERT: B 148 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: C 1 MET cc_start: 0.3922 (pmm) cc_final: 0.2800 (ppp) REVERT: C 8 MET cc_start: 0.1093 (mmm) cc_final: 0.0707 (mtm) REVERT: C 33 MET cc_start: 0.1111 (ttp) cc_final: 0.0827 (ttp) REVERT: C 51 MET cc_start: 0.3924 (mmp) cc_final: 0.3304 (tpp) REVERT: C 111 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8251 (mp10) REVERT: D 51 MET cc_start: 0.2003 (mmm) cc_final: 0.1544 (tpp) REVERT: D 104 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8120 (tm-30) REVERT: D 111 GLN cc_start: 0.8779 (pp30) cc_final: 0.8375 (pt0) REVERT: E 99 ARG cc_start: 0.7590 (mmm-85) cc_final: 0.6855 (ttt-90) REVERT: E 109 ARG cc_start: 0.8023 (ttm-80) cc_final: 0.7480 (tpp80) REVERT: E 110 ARG cc_start: 0.7561 (ttt-90) cc_final: 0.7197 (tmt170) REVERT: E 132 ARG cc_start: 0.7764 (tpt90) cc_final: 0.7435 (mmp80) REVERT: E 149 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7510 (tpt) REVERT: E 155 ARG cc_start: 0.6575 (ttp80) cc_final: 0.6150 (ttp80) REVERT: F 98 GLN cc_start: 0.8137 (tt0) cc_final: 0.7890 (tp40) REVERT: F 99 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.6946 (ttt-90) REVERT: F 114 MET cc_start: 0.8726 (tmm) cc_final: 0.8484 (tmm) REVERT: F 132 ARG cc_start: 0.7925 (tpt90) cc_final: 0.7539 (mmp80) REVERT: F 149 MET cc_start: 0.8824 (tpt) cc_final: 0.8104 (ptt) REVERT: G 64 PHE cc_start: 0.9211 (m-80) cc_final: 0.9004 (m-80) REVERT: H 149 MET cc_start: 0.8089 (ttp) cc_final: 0.7728 (ptt) REVERT: I 111 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8403 (mp10) REVERT: I 148 TYR cc_start: 0.9037 (OUTLIER) cc_final: 0.8465 (m-10) outliers start: 176 outliers final: 116 residues processed: 568 average time/residue: 0.4404 time to fit residues: 387.9920 Evaluate side-chains 549 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 421 time to evaluate : 3.585 ------------------------------------------------------------------------------- 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 158 ILE Chi-restraints excluded: chain R residue 199 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 251 MET Chi-restraints excluded: chain R residue 305 LYS Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 168 THR Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 225 GLU 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 66 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 140 SER Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 222 ASP 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 158 ILE Chi-restraints excluded: chain L residue 199 SER 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 46 MET Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 229 VAL 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 47 ASN 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 140 SER Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 48 VAL Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain O residue 158 ILE Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 215 GLN Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 158 ILE Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 162 GLU 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 212 THR Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain Q residue 140 SER Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain Q residue 319 GLN 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 35 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 111 GLN 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 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 84 ILE 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 G residue 19 LEU Chi-restraints excluded: chain G residue 62 SER Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain H residue 33 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 261 optimal weight: 1.9990 chunk 390 optimal weight: 7.9990 chunk 255 optimal weight: 0.6980 chunk 306 optimal weight: 2.9990 chunk 373 optimal weight: 10.0000 chunk 28 optimal weight: 0.6980 chunk 323 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 265 optimal weight: 5.9990 chunk 341 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 159 ASN J 176 ASN K 176 ASN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 176 ASN N 176 ASN ** P 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 238 GLN B 86 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN D 121 GLN F 111 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.206470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113547 restraints weight = 48432.315| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.76 r_work: 0.3021 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31860 Z= 0.196 Angle : 0.570 8.567 42867 Z= 0.304 Chirality : 0.037 0.165 4635 Planarity : 0.003 0.075 5985 Dihedral : 3.951 49.629 4585 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.36 % Favored : 93.43 % Rotamer: Outliers : 4.10 % Allowed : 28.58 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.14), residues: 4122 helix: 2.71 (0.10), residues: 2979 sheet: -3.12 (0.52), residues: 90 loop : -3.46 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 77 HIS 0.002 0.001 HIS K 198 PHE 0.027 0.001 PHE E 112 TYR 0.012 0.001 TYR G 116 ARG 0.008 0.000 ARG O 220 Details of bonding type rmsd hydrogen bonds : bond 0.07437 ( 2290) hydrogen bonds : angle 3.74212 ( 6843) covalent geometry : bond 0.00432 (31860) covalent geometry : angle 0.56967 (42867) *********************** 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 580 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 448 time to evaluate : 3.608 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 260 MET cc_start: 0.0026 (mmp) cc_final: -0.0708 (mmp) REVERT: R 305 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7108 (ptpp) REVERT: J 90 MET cc_start: 0.9315 (ttm) cc_final: 0.9082 (ttm) REVERT: J 165 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8525 (ttmm) REVERT: J 220 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7806 (ttp80) REVERT: K 36 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7590 (tt) REVERT: K 42 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7515 (mtm-85) REVERT: L 38 ASP cc_start: 0.8154 (p0) cc_final: 0.7385 (t70) REVERT: L 90 MET cc_start: 0.9413 (mtp) cc_final: 0.9172 (mtp) REVERT: L 221 ARG cc_start: 0.8290 (ttm110) cc_final: 0.8028 (ttm110) REVERT: L 260 MET cc_start: 0.0557 (mmp) cc_final: -0.1794 (tmm) REVERT: M 221 ARG cc_start: 0.8454 (ttm110) cc_final: 0.7982 (ttm110) REVERT: N 95 ASP cc_start: 0.8833 (t70) cc_final: 0.8277 (t70) REVERT: N 101 ASP cc_start: 0.8813 (p0) cc_final: 0.8374 (p0) REVERT: N 126 GLU cc_start: 0.8873 (tt0) cc_final: 0.8573 (tm-30) REVERT: O 36 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7248 (tt) REVERT: O 95 ASP cc_start: 0.9063 (t0) cc_final: 0.8593 (t0) REVERT: O 176 ASN cc_start: 0.8472 (t0) cc_final: 0.8251 (m110) REVERT: O 214 GLU cc_start: 0.8357 (mm-30) cc_final: 0.7956 (mt-10) REVERT: O 221 ARG cc_start: 0.8687 (ttm-80) cc_final: 0.8475 (ttm110) REVERT: P 42 ARG cc_start: 0.8549 (mmm-85) cc_final: 0.8274 (mmm-85) REVERT: P 101 ASP cc_start: 0.8857 (p0) cc_final: 0.8643 (p0) REVERT: P 135 GLN cc_start: 0.8497 (tt0) cc_final: 0.8257 (tp40) REVERT: P 188 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8039 (mm-40) REVERT: P 215 GLN cc_start: 0.8787 (tt0) cc_final: 0.8372 (tt0) REVERT: Q 42 ARG cc_start: 0.8270 (mtt90) cc_final: 0.7820 (mpt-90) REVERT: Q 101 ASP cc_start: 0.8799 (p0) cc_final: 0.8527 (p0) REVERT: Q 185 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8136 (tm-30) REVERT: Q 214 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8279 (tt0) REVERT: Q 260 MET cc_start: -0.2350 (mmp) cc_final: -0.2969 (tmm) REVERT: A 3 TYR cc_start: 0.0947 (OUTLIER) cc_final: -0.0158 (p90) REVERT: A 99 ARG cc_start: 0.7731 (mmm-85) cc_final: 0.6973 (ttt-90) REVERT: A 110 ARG cc_start: 0.7900 (ttt-90) cc_final: 0.7583 (tmt170) REVERT: A 132 ARG cc_start: 0.6930 (tpt90) cc_final: 0.6106 (mmp-170) REVERT: B 104 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7702 (tm-30) REVERT: B 111 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7936 (pp30) REVERT: B 152 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.7759 (p0) REVERT: C 1 MET cc_start: 0.4225 (pmm) cc_final: 0.3202 (ppp) REVERT: C 8 MET cc_start: 0.1089 (mmm) cc_final: 0.0703 (mtm) REVERT: C 33 MET cc_start: 0.1179 (ttp) cc_final: 0.0864 (ttp) REVERT: C 51 MET cc_start: 0.3403 (mmp) cc_final: 0.1795 (mtt) REVERT: C 111 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8357 (mp10) REVERT: C 146 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7867 (t0) REVERT: C 148 TYR cc_start: 0.8704 (OUTLIER) cc_final: 0.8480 (m-80) REVERT: D 51 MET cc_start: 0.2351 (mmm) cc_final: 0.1739 (tpp) REVERT: D 104 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7974 (tm-30) REVERT: D 111 GLN cc_start: 0.8822 (pp30) cc_final: 0.8337 (pt0) REVERT: E 35 MET cc_start: -0.1754 (pmm) cc_final: -0.2087 (ptt) REVERT: E 99 ARG cc_start: 0.7590 (mmm-85) cc_final: 0.6896 (ttt-90) REVERT: E 109 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7375 (tpp80) REVERT: E 110 ARG cc_start: 0.7615 (ttt-90) cc_final: 0.7199 (tmt170) REVERT: E 132 ARG cc_start: 0.7801 (tpt90) cc_final: 0.7474 (mmp80) REVERT: E 149 MET cc_start: 0.7935 (mmp) cc_final: 0.7504 (tpt) REVERT: F 98 GLN cc_start: 0.8107 (tt0) cc_final: 0.7862 (tp40) REVERT: F 99 ARG cc_start: 0.7656 (mmm-85) cc_final: 0.6919 (ttt-90) REVERT: F 114 MET cc_start: 0.8703 (tmm) cc_final: 0.8452 (tmm) REVERT: F 132 ARG cc_start: 0.7908 (tpt90) cc_final: 0.7570 (mmp80) REVERT: H 149 MET cc_start: 0.7965 (ttp) cc_final: 0.7549 (ptt) REVERT: I 148 TYR cc_start: 0.9028 (OUTLIER) cc_final: 0.8341 (m-10) outliers start: 132 outliers final: 83 residues processed: 552 average time/residue: 0.4515 time to fit residues: 383.6825 Evaluate side-chains 540 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 445 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 48 VAL 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 229 VAL Chi-restraints excluded: chain R residue 305 LYS Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 165 LYS Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 233 ILE 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 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 166 GLU Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 46 MET Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 124 GLN Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 229 VAL Chi-restraints excluded: chain M residue 270 MET 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 201 SER Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain P residue 78 ASP 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 317 ILE 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 140 SER Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain Q residue 229 VAL Chi-restraints excluded: chain Q residue 319 GLN Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 31 LEU 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 111 GLN Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 131 GLN 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 103 ASP Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 148 TYR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 121 GLN 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 F residue 40 VAL Chi-restraints excluded: chain F 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 103 ASP Chi-restraints excluded: chain H residue 111 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 235 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 175 optimal weight: 30.0000 chunk 43 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 302 optimal weight: 0.9990 chunk 330 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 310 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN J 159 ASN J 176 ASN K 176 ASN K 238 GLN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 176 ASN N 176 ASN P 156 GLN P 176 ASN B 86 GLN B 152 ASN F 111 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.211651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117646 restraints weight = 48070.184| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.03 r_work: 0.3043 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31860 Z= 0.157 Angle : 0.541 9.826 42867 Z= 0.287 Chirality : 0.036 0.158 4635 Planarity : 0.003 0.070 5985 Dihedral : 3.800 48.344 4585 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.60 % Favored : 93.16 % Rotamer: Outliers : 3.88 % Allowed : 28.71 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.14), residues: 4122 helix: 2.91 (0.10), residues: 2970 sheet: -3.06 (0.52), residues: 90 loop : -3.44 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 77 HIS 0.000 0.000 HIS M 198 PHE 0.030 0.001 PHE E 112 TYR 0.011 0.001 TYR B 148 ARG 0.013 0.000 ARG M 216 Details of bonding type rmsd hydrogen bonds : bond 0.06982 ( 2290) hydrogen bonds : angle 3.58024 ( 6843) covalent geometry : bond 0.00328 (31860) covalent geometry : angle 0.54080 (42867) *********************** 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 578 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 453 time to evaluate : 3.280 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: R 126 GLU cc_start: 0.8945 (tt0) cc_final: 0.8645 (tm-30) REVERT: R 260 MET cc_start: 0.0309 (mmp) cc_final: -0.0456 (mmp) REVERT: R 305 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7068 (ptpp) REVERT: J 36 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7862 (tt) REVERT: J 42 ARG cc_start: 0.7741 (ptp90) cc_final: 0.7491 (ptp90) REVERT: J 165 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8514 (ttmm) REVERT: J 185 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8202 (tm-30) REVERT: J 220 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7859 (ttp80) REVERT: K 36 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7584 (tt) REVERT: K 90 MET cc_start: 0.8580 (mtp) cc_final: 0.8294 (mtt) REVERT: L 38 ASP cc_start: 0.8074 (p0) cc_final: 0.7370 (t70) REVERT: L 90 MET cc_start: 0.9371 (mtp) cc_final: 0.9121 (mtp) REVERT: L 92 MET cc_start: 0.9034 (tpp) cc_final: 0.8802 (mmm) REVERT: L 126 GLU cc_start: 0.8991 (tt0) cc_final: 0.8627 (tm-30) REVERT: L 221 ARG cc_start: 0.8229 (ttm110) cc_final: 0.7975 (ttm110) REVERT: L 260 MET cc_start: 0.0595 (mmp) cc_final: -0.1796 (tmm) REVERT: M 42 ARG cc_start: 0.8607 (ptm160) cc_final: 0.7792 (ptp90) REVERT: M 221 ARG cc_start: 0.8420 (ttm110) cc_final: 0.8007 (ttm110) REVERT: N 95 ASP cc_start: 0.8733 (t70) cc_final: 0.8117 (t70) REVERT: N 101 ASP cc_start: 0.8824 (p0) cc_final: 0.8344 (p0) REVERT: N 126 GLU cc_start: 0.8834 (tt0) cc_final: 0.8535 (tm-30) REVERT: O 36 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7235 (tt) REVERT: O 95 ASP cc_start: 0.9046 (t0) cc_final: 0.8653 (t0) REVERT: O 214 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7955 (mt-10) REVERT: P 42 ARG cc_start: 0.8527 (mmm-85) cc_final: 0.8227 (mmm-85) REVERT: P 101 ASP cc_start: 0.8879 (p0) cc_final: 0.8670 (p0) REVERT: P 135 GLN cc_start: 0.8523 (tt0) cc_final: 0.8323 (tp40) REVERT: P 188 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7965 (mm-40) REVERT: P 215 GLN cc_start: 0.8723 (tt0) cc_final: 0.8366 (tt0) REVERT: P 221 ARG cc_start: 0.8653 (tpp80) cc_final: 0.8238 (ttm110) REVERT: Q 42 ARG cc_start: 0.8197 (mtt90) cc_final: 0.7738 (mpt-90) REVERT: Q 56 GLU cc_start: 0.8856 (tp30) cc_final: 0.8630 (tp30) REVERT: Q 90 MET cc_start: 0.9242 (mtp) cc_final: 0.8867 (mtp) REVERT: Q 101 ASP cc_start: 0.8812 (p0) cc_final: 0.8524 (p0) REVERT: Q 185 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8123 (tm-30) REVERT: Q 214 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8294 (tt0) REVERT: Q 260 MET cc_start: -0.2360 (mmp) cc_final: -0.2961 (tmm) REVERT: A 3 TYR cc_start: 0.0935 (OUTLIER) cc_final: -0.0150 (p90) REVERT: A 99 ARG cc_start: 0.7561 (mmm-85) cc_final: 0.6794 (ttt-90) REVERT: A 110 ARG cc_start: 0.7871 (ttt-90) cc_final: 0.7544 (tmt170) REVERT: A 132 ARG cc_start: 0.6888 (tpt90) cc_final: 0.6081 (mmp-170) REVERT: B 35 MET cc_start: 0.0174 (OUTLIER) cc_final: -0.0951 (tmm) REVERT: B 99 ARG cc_start: 0.7301 (mmm-85) cc_final: 0.6666 (tpp-160) REVERT: B 104 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7661 (tm-30) REVERT: B 111 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7974 (pp30) REVERT: B 149 MET cc_start: 0.7859 (mmm) cc_final: 0.7384 (ptt) REVERT: C 1 MET cc_start: 0.4072 (pmm) cc_final: 0.3116 (ppp) REVERT: C 8 MET cc_start: 0.1084 (mmm) cc_final: 0.0700 (mtm) REVERT: C 33 MET cc_start: 0.1089 (ttp) cc_final: 0.0766 (ttp) REVERT: C 51 MET cc_start: 0.3401 (mmp) cc_final: 0.2091 (mtm) REVERT: C 111 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8311 (mp10) REVERT: C 114 MET cc_start: 0.8630 (ttp) cc_final: 0.8421 (tmm) REVERT: C 148 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8496 (m-80) REVERT: D 51 MET cc_start: 0.2480 (mmm) cc_final: 0.2192 (tpt) REVERT: D 104 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7967 (tm-30) REVERT: D 111 GLN cc_start: 0.8872 (pp30) cc_final: 0.8407 (pt0) REVERT: E 35 MET cc_start: -0.1887 (pmm) cc_final: -0.2196 (ptt) REVERT: E 99 ARG cc_start: 0.7561 (mmm-85) cc_final: 0.6874 (ttt-90) REVERT: E 109 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7303 (tpp80) REVERT: E 110 ARG cc_start: 0.7510 (ttt-90) cc_final: 0.7107 (tmt170) REVERT: E 132 ARG cc_start: 0.7852 (tpt90) cc_final: 0.7518 (mmp80) REVERT: E 149 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7502 (tpt) REVERT: F 98 GLN cc_start: 0.8032 (tt0) cc_final: 0.7807 (tp40) REVERT: F 99 ARG cc_start: 0.7625 (mmm-85) cc_final: 0.6891 (ttt-90) REVERT: F 114 MET cc_start: 0.8692 (tmm) cc_final: 0.8472 (tmm) REVERT: F 132 ARG cc_start: 0.7914 (tpt90) cc_final: 0.7565 (mmp80) REVERT: G 109 ARG cc_start: 0.7400 (tpp80) cc_final: 0.7074 (ttm-80) REVERT: H 111 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8065 (mp10) REVERT: H 149 MET cc_start: 0.8059 (ttp) cc_final: 0.7786 (ptt) REVERT: I 148 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.8328 (m-10) outliers start: 125 outliers final: 78 residues processed: 548 average time/residue: 0.4532 time to fit residues: 380.2085 Evaluate side-chains 526 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 434 time to evaluate : 3.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 48 VAL 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 229 VAL Chi-restraints excluded: chain R residue 305 LYS Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 165 LYS Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 233 ILE 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 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 L residue 66 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 305 LYS Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 124 GLN 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 66 VAL Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR 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 188 GLN Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 317 ILE Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 140 SER Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain Q residue 229 VAL Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 131 GLN 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 148 TYR 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 149 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL 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 H residue 111 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 131 optimal weight: 1.9990 chunk 378 optimal weight: 4.9990 chunk 397 optimal weight: 0.9980 chunk 361 optimal weight: 20.0000 chunk 401 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 270 optimal weight: 20.0000 chunk 28 optimal weight: 0.4980 chunk 384 optimal weight: 0.7980 chunk 377 optimal weight: 10.0000 chunk 341 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN J 106 GLN K 176 ASN M 156 GLN M 176 ASN N 176 ASN 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 = 0.4444 r_free = 0.4444 target = 0.209556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114069 restraints weight = 49963.473| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.86 r_work: 0.3021 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 31860 Z= 0.196 Angle : 0.572 12.018 42867 Z= 0.305 Chirality : 0.037 0.158 4635 Planarity : 0.003 0.068 5985 Dihedral : 3.808 41.514 4585 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.62 % Favored : 93.13 % Rotamer: Outliers : 4.22 % Allowed : 28.46 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.14), residues: 4122 helix: 2.85 (0.10), residues: 2979 sheet: -3.12 (0.52), residues: 90 loop : -3.42 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 77 HIS 0.001 0.001 HIS M 198 PHE 0.025 0.001 PHE E 112 TYR 0.008 0.001 TYR J 79 ARG 0.010 0.000 ARG N 220 Details of bonding type rmsd hydrogen bonds : bond 0.07254 ( 2290) hydrogen bonds : angle 3.64578 ( 6843) covalent geometry : bond 0.00437 (31860) covalent geometry : angle 0.57240 (42867) *********************** 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 577 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 441 time to evaluate : 3.193 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 260 MET cc_start: 0.0289 (mmp) cc_final: -0.0457 (mmp) REVERT: R 305 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.6971 (ptpp) REVERT: J 90 MET cc_start: 0.9206 (ttm) cc_final: 0.8750 (ttm) REVERT: J 185 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8189 (tm-30) REVERT: J 220 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7796 (ttp80) REVERT: K 36 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7607 (tt) REVERT: K 90 MET cc_start: 0.8526 (mtp) cc_final: 0.8231 (mtt) REVERT: K 214 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8368 (mt-10) REVERT: L 38 ASP cc_start: 0.8078 (p0) cc_final: 0.7406 (t70) REVERT: L 90 MET cc_start: 0.9411 (mtp) cc_final: 0.9113 (mtp) REVERT: L 101 ASP cc_start: 0.8914 (p0) cc_final: 0.8511 (p0) REVERT: L 221 ARG cc_start: 0.8240 (ttm110) cc_final: 0.7967 (ttm110) REVERT: L 260 MET cc_start: 0.0569 (mmp) cc_final: -0.1892 (tmm) REVERT: N 101 ASP cc_start: 0.8825 (p0) cc_final: 0.8313 (p0) REVERT: N 119 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8557 (ttmm) REVERT: N 126 GLU cc_start: 0.8821 (tt0) cc_final: 0.8521 (tm-30) REVERT: O 36 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7177 (tt) REVERT: O 95 ASP cc_start: 0.9079 (t0) cc_final: 0.8636 (t0) REVERT: O 176 ASN cc_start: 0.8514 (t0) cc_final: 0.8306 (m110) REVERT: O 214 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7983 (mt-10) REVERT: P 101 ASP cc_start: 0.8884 (p0) cc_final: 0.8680 (p0) REVERT: P 135 GLN cc_start: 0.8514 (tt0) cc_final: 0.8313 (tp40) REVERT: P 188 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.7967 (mm-40) REVERT: P 221 ARG cc_start: 0.8760 (tpp80) cc_final: 0.8353 (ttm110) REVERT: Q 42 ARG cc_start: 0.8282 (mtt90) cc_final: 0.7799 (mpt-90) REVERT: Q 56 GLU cc_start: 0.8848 (tp30) cc_final: 0.8592 (tp30) REVERT: Q 90 MET cc_start: 0.9359 (mtp) cc_final: 0.8926 (mtp) REVERT: Q 101 ASP cc_start: 0.8808 (p0) cc_final: 0.8501 (p0) REVERT: Q 185 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8103 (tm-30) REVERT: Q 214 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8278 (tt0) REVERT: Q 260 MET cc_start: -0.2298 (mmp) cc_final: -0.2932 (tmm) REVERT: A 3 TYR cc_start: 0.0943 (OUTLIER) cc_final: -0.0132 (p90) REVERT: B 35 MET cc_start: 0.0201 (OUTLIER) cc_final: -0.0924 (tmm) REVERT: B 111 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7758 (mt0) REVERT: B 149 MET cc_start: 0.7921 (mmm) cc_final: 0.7376 (ptt) REVERT: C 1 MET cc_start: 0.4158 (pmm) cc_final: 0.3153 (ppp) REVERT: C 8 MET cc_start: 0.1087 (mmm) cc_final: 0.0705 (mtm) REVERT: C 33 MET cc_start: 0.1079 (ttp) cc_final: 0.0741 (ttp) REVERT: C 51 MET cc_start: 0.3273 (mmp) cc_final: 0.2071 (mtm) REVERT: C 111 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8322 (mp10) REVERT: C 146 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7843 (t0) REVERT: C 148 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8553 (m-80) REVERT: D 51 MET cc_start: 0.2474 (mmm) cc_final: 0.2201 (tpt) REVERT: D 104 GLN cc_start: 0.8328 (tm-30) cc_final: 0.8125 (tm-30) REVERT: D 111 GLN cc_start: 0.8866 (pp30) cc_final: 0.8457 (pt0) REVERT: E 35 MET cc_start: -0.1887 (pmm) cc_final: -0.2194 (ptt) REVERT: E 99 ARG cc_start: 0.7573 (mmm-85) cc_final: 0.6867 (ttt-90) REVERT: E 109 ARG cc_start: 0.7828 (ttm-80) cc_final: 0.7268 (tpp80) REVERT: E 132 ARG cc_start: 0.7839 (tpt90) cc_final: 0.7486 (mmp80) REVERT: E 149 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7513 (tpt) REVERT: F 98 GLN cc_start: 0.8031 (tt0) cc_final: 0.7804 (tp40) REVERT: F 114 MET cc_start: 0.8617 (tmm) cc_final: 0.8411 (tmm) REVERT: H 111 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8094 (mp10) REVERT: I 111 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8734 (tp40) REVERT: I 148 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.8473 (m-10) outliers start: 136 outliers final: 103 residues processed: 545 average time/residue: 0.4433 time to fit residues: 376.6107 Evaluate side-chains 552 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 435 time to evaluate : 3.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 48 VAL 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 201 SER Chi-restraints excluded: chain R residue 229 VAL 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 229 VAL Chi-restraints excluded: chain J residue 233 ILE 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 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 199 SER 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 48 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 305 LYS Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 124 GLN Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 47 ASN 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 201 SER Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 212 THR 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 317 ILE 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 140 SER Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain Q residue 229 VAL Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 31 LEU 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 1 MET Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 114 MET 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 146 ASP Chi-restraints excluded: chain C residue 148 TYR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 121 GLN 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 149 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 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 35 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 H residue 111 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 193 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 397 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 238 optimal weight: 3.9990 chunk 190 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 337 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 232 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN J 106 GLN J 176 ASN K 176 ASN M 176 ASN N 176 ASN P 176 ASN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 GLN F 111 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.208372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.113888 restraints weight = 49754.628| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.88 r_work: 0.3058 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31860 Z= 0.154 Angle : 0.554 11.638 42867 Z= 0.293 Chirality : 0.035 0.158 4635 Planarity : 0.003 0.048 5985 Dihedral : 3.708 40.705 4585 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.48 % Favored : 93.28 % Rotamer: Outliers : 3.57 % Allowed : 28.90 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.14), residues: 4122 helix: 3.00 (0.10), residues: 2970 sheet: None (None), residues: 0 loop : -3.23 (0.15), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 77 HIS 0.000 0.000 HIS J 198 PHE 0.030 0.001 PHE E 112 TYR 0.010 0.001 TYR L 62 ARG 0.011 0.000 ARG L 220 Details of bonding type rmsd hydrogen bonds : bond 0.06812 ( 2290) hydrogen bonds : angle 3.50486 ( 6843) covalent geometry : bond 0.00322 (31860) covalent geometry : angle 0.55436 (42867) *********************** 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 551 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 436 time to evaluate : 3.426 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: 0.8935 (tt0) cc_final: 0.8647 (tm-30) REVERT: R 260 MET cc_start: 0.0320 (mmp) cc_final: -0.0417 (mmp) REVERT: R 305 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.6885 (ptpp) REVERT: J 42 ARG cc_start: 0.7673 (ptp90) cc_final: 0.7471 (ptp90) REVERT: J 90 MET cc_start: 0.9122 (ttm) cc_final: 0.8703 (ttm) REVERT: J 185 GLN cc_start: 0.8392 (tm-30) cc_final: 0.8149 (tm-30) REVERT: J 220 ARG cc_start: 0.8171 (ttm110) cc_final: 0.7838 (ttp80) REVERT: K 36 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7614 (tt) REVERT: K 90 MET cc_start: 0.8496 (mtp) cc_final: 0.8226 (mtt) REVERT: K 214 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8330 (mt-10) REVERT: K 270 MET cc_start: 0.3937 (tpp) cc_final: 0.3722 (tpp) REVERT: L 38 ASP cc_start: 0.8024 (p0) cc_final: 0.7376 (p0) REVERT: L 42 ARG cc_start: 0.8256 (mmt90) cc_final: 0.7752 (mpt-90) REVERT: L 90 MET cc_start: 0.9365 (mtp) cc_final: 0.9125 (mtp) REVERT: L 101 ASP cc_start: 0.8842 (p0) cc_final: 0.8474 (p0) REVERT: L 126 GLU cc_start: 0.8969 (tt0) cc_final: 0.8602 (tm-30) REVERT: L 260 MET cc_start: 0.0628 (mmp) cc_final: 0.0037 (mmp) REVERT: N 101 ASP cc_start: 0.8734 (p0) cc_final: 0.8254 (p0) REVERT: N 119 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8557 (ttmm) REVERT: O 36 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7158 (tt) REVERT: O 95 ASP cc_start: 0.9034 (t0) cc_final: 0.8663 (t0) REVERT: O 214 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7996 (mt-10) REVERT: P 188 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7939 (mm-40) REVERT: P 221 ARG cc_start: 0.8623 (tpp80) cc_final: 0.8229 (ttm110) REVERT: Q 42 ARG cc_start: 0.8168 (mtt90) cc_final: 0.7719 (mpt-90) REVERT: Q 56 GLU cc_start: 0.8830 (tp30) cc_final: 0.8586 (tp30) REVERT: Q 90 MET cc_start: 0.9303 (mtp) cc_final: 0.8907 (mtp) REVERT: Q 101 ASP cc_start: 0.8814 (p0) cc_final: 0.8509 (p0) REVERT: Q 185 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8098 (tm-30) REVERT: Q 214 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8296 (tt0) REVERT: Q 260 MET cc_start: -0.2067 (mmp) cc_final: -0.2722 (tmm) REVERT: A 3 TYR cc_start: 0.0962 (OUTLIER) cc_final: -0.0125 (p90) REVERT: B 35 MET cc_start: 0.0211 (OUTLIER) cc_final: -0.0907 (tmm) REVERT: B 104 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7777 (tm-30) REVERT: B 111 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: C 1 MET cc_start: 0.4103 (pmm) cc_final: 0.3208 (ppp) REVERT: C 8 MET cc_start: 0.1088 (mmm) cc_final: 0.0705 (mtm) REVERT: C 33 MET cc_start: 0.1126 (ttp) cc_final: 0.0777 (ttp) REVERT: C 51 MET cc_start: 0.3716 (mmp) cc_final: 0.2466 (mtm) REVERT: C 111 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8307 (mp10) REVERT: C 148 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.8544 (m-80) REVERT: D 51 MET cc_start: 0.2428 (mmm) cc_final: 0.2164 (tpt) REVERT: D 104 GLN cc_start: 0.8313 (tm-30) cc_final: 0.8105 (tm-30) REVERT: D 111 GLN cc_start: 0.8853 (pp30) cc_final: 0.8468 (pt0) REVERT: E 35 MET cc_start: -0.1886 (pmm) cc_final: -0.2194 (ptt) REVERT: E 99 ARG cc_start: 0.7484 (mmm-85) cc_final: 0.6773 (ttt-90) REVERT: E 109 ARG cc_start: 0.7812 (ttm-80) cc_final: 0.7266 (tpp80) REVERT: E 132 ARG cc_start: 0.7916 (tpt90) cc_final: 0.7545 (mmp80) REVERT: E 149 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7544 (tpt) REVERT: F 98 GLN cc_start: 0.8011 (tt0) cc_final: 0.7799 (tp40) REVERT: F 99 ARG cc_start: 0.7612 (mmm-85) cc_final: 0.6873 (ttt-90) REVERT: F 132 ARG cc_start: 0.7999 (tpt90) cc_final: 0.7642 (mmp80) REVERT: H 111 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8063 (mp10) REVERT: I 111 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8722 (tp40) REVERT: I 148 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.8338 (m-10) outliers start: 115 outliers final: 94 residues processed: 522 average time/residue: 0.4418 time to fit residues: 357.8809 Evaluate side-chains 541 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 434 time to evaluate : 3.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 48 VAL 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 229 VAL Chi-restraints excluded: chain R residue 305 LYS 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 233 ILE 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 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 199 SER 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 48 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 305 LYS Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 124 GLN Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 47 ASN 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 201 SER Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 212 THR 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 317 ILE 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 140 SER Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain Q residue 229 VAL Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 31 LEU 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 1 MET Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 114 MET 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 148 TYR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 82 LEU 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 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 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 111 GLN 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 Chi-restraints excluded: chain I residue 149 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 402 optimal weight: 2.9990 chunk 360 optimal weight: 0.0980 chunk 121 optimal weight: 1.9990 chunk 327 optimal weight: 6.9990 chunk 356 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 259 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 385 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN J 106 GLN M 176 ASN Q 286 ASN D 121 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 = 0.4453 r_free = 0.4453 target = 0.211227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117523 restraints weight = 49148.460| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.23 r_work: 0.3003 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 31860 Z= 0.190 Angle : 0.589 11.878 42867 Z= 0.311 Chirality : 0.037 0.158 4635 Planarity : 0.003 0.057 5985 Dihedral : 3.747 40.377 4583 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.48 % Favored : 93.28 % Rotamer: Outliers : 3.79 % Allowed : 29.08 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.14), residues: 4122 helix: 2.89 (0.10), residues: 2979 sheet: None (None), residues: 0 loop : -3.23 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 77 HIS 0.001 0.000 HIS J 198 PHE 0.031 0.001 PHE E 112 TYR 0.012 0.001 TYR E 116 ARG 0.009 0.000 ARG Q 220 Details of bonding type rmsd hydrogen bonds : bond 0.07191 ( 2290) hydrogen bonds : angle 3.60047 ( 6843) covalent geometry : bond 0.00421 (31860) covalent geometry : angle 0.58927 (42867) *********************** 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 553 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 431 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 260 MET cc_start: 0.0296 (mmp) cc_final: -0.0430 (mmp) REVERT: R 305 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6944 (ptpp) REVERT: J 90 MET cc_start: 0.9186 (ttm) cc_final: 0.8740 (ttm) REVERT: J 185 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8188 (tm-30) REVERT: J 220 ARG cc_start: 0.8181 (ttm110) cc_final: 0.7846 (ttp80) REVERT: K 36 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7631 (tt) REVERT: K 90 MET cc_start: 0.8613 (mtp) cc_final: 0.8337 (mtt) REVERT: K 214 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8342 (mt-10) REVERT: K 270 MET cc_start: 0.3988 (tpp) cc_final: 0.3754 (tpp) REVERT: L 38 ASP cc_start: 0.8048 (p0) cc_final: 0.7294 (p0) REVERT: L 42 ARG cc_start: 0.8324 (mmt90) cc_final: 0.7824 (mpt-90) REVERT: L 90 MET cc_start: 0.9406 (mtp) cc_final: 0.9195 (mmm) REVERT: N 101 ASP cc_start: 0.8801 (p0) cc_final: 0.8324 (p0) REVERT: N 119 LYS cc_start: 0.8811 (mtpt) cc_final: 0.8595 (ttmm) REVERT: N 126 GLU cc_start: 0.8847 (tt0) cc_final: 0.8517 (tm-30) REVERT: N 130 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7197 (mtt180) REVERT: O 36 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7200 (tt) REVERT: O 42 ARG cc_start: 0.8065 (ptp90) cc_final: 0.7755 (ptp90) REVERT: O 95 ASP cc_start: 0.9091 (t0) cc_final: 0.8715 (t0) REVERT: O 176 ASN cc_start: 0.8500 (t0) cc_final: 0.8293 (m110) REVERT: O 214 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8042 (mt-10) REVERT: P 188 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7982 (mm-40) REVERT: P 216 ARG cc_start: 0.8151 (mtp180) cc_final: 0.7807 (mtp180) REVERT: P 221 ARG cc_start: 0.8695 (tpp80) cc_final: 0.8291 (ttm110) REVERT: Q 42 ARG cc_start: 0.8301 (mtt90) cc_final: 0.7933 (mtm-85) REVERT: Q 56 GLU cc_start: 0.8879 (tp30) cc_final: 0.8626 (tp30) REVERT: Q 101 ASP cc_start: 0.8837 (p0) cc_final: 0.8527 (p0) REVERT: Q 185 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8095 (tm-30) REVERT: Q 214 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8308 (tt0) REVERT: Q 260 MET cc_start: -0.2048 (mmp) cc_final: -0.2740 (tmm) REVERT: A 3 TYR cc_start: 0.0959 (OUTLIER) cc_final: -0.0110 (p90) REVERT: B 35 MET cc_start: 0.0225 (OUTLIER) cc_final: -0.0833 (tmm) REVERT: B 104 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7775 (tm-30) REVERT: B 111 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.7816 (mt0) REVERT: B 149 MET cc_start: 0.7918 (mmm) cc_final: 0.7193 (ptt) REVERT: C 1 MET cc_start: 0.4021 (pmm) cc_final: 0.3141 (ppp) REVERT: C 8 MET cc_start: 0.1091 (mmm) cc_final: 0.0713 (mtm) REVERT: C 51 MET cc_start: 0.3785 (mmp) cc_final: 0.2584 (mtm) REVERT: C 111 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8297 (mp10) REVERT: C 148 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.8537 (m-80) REVERT: D 51 MET cc_start: 0.2464 (mmm) cc_final: 0.2202 (tpt) REVERT: D 99 ARG cc_start: 0.7374 (mmm-85) cc_final: 0.7045 (ttt180) REVERT: D 109 ARG cc_start: 0.7698 (tpp80) cc_final: 0.7327 (tpp80) REVERT: D 110 ARG cc_start: 0.7149 (ppt170) cc_final: 0.6942 (ppt170) REVERT: D 111 GLN cc_start: 0.8870 (pp30) cc_final: 0.8541 (pt0) REVERT: E 35 MET cc_start: -0.1903 (pmm) cc_final: -0.2138 (ptt) REVERT: E 99 ARG cc_start: 0.7553 (mmm-85) cc_final: 0.6876 (ttt-90) REVERT: E 109 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.7323 (tpp80) REVERT: E 132 ARG cc_start: 0.7906 (tpt90) cc_final: 0.7541 (mmp80) REVERT: E 149 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7552 (tpt) REVERT: H 111 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8026 (mp10) REVERT: I 111 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8694 (tp40) REVERT: I 148 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8476 (m-10) outliers start: 122 outliers final: 102 residues processed: 524 average time/residue: 0.4334 time to fit residues: 350.6847 Evaluate side-chains 546 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 430 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 59 THR 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 229 VAL 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 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 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 199 SER 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 48 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 305 LYS Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 124 GLN Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 130 ARG Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 140 SER Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 212 THR 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 317 ILE 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 140 SER Chi-restraints excluded: chain Q residue 163 ILE Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain Q residue 229 VAL Chi-restraints excluded: chain Q residue 251 MET Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 31 LEU 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 35 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 114 MET 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 148 TYR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 82 LEU 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 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 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 111 GLN 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 260 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 133 optimal weight: 0.4980 chunk 77 optimal weight: 0.6980 chunk 332 optimal weight: 0.0570 chunk 36 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 233 optimal weight: 0.0000 overall best weight: 0.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN J 106 GLN K 176 ASN M 176 ASN N 176 ASN D 121 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.210261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118804 restraints weight = 48945.872| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.85 r_work: 0.3114 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31860 Z= 0.136 Angle : 0.562 11.674 42867 Z= 0.291 Chirality : 0.035 0.158 4635 Planarity : 0.003 0.058 5985 Dihedral : 3.598 38.414 4583 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.11 % Favored : 93.64 % Rotamer: Outliers : 2.70 % Allowed : 30.07 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.14), residues: 4122 helix: 3.08 (0.10), residues: 2970 sheet: None (None), residues: 0 loop : -3.19 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 77 HIS 0.001 0.000 HIS K 198 PHE 0.034 0.001 PHE E 112 TYR 0.012 0.001 TYR L 62 ARG 0.014 0.000 ARG R 220 Details of bonding type rmsd hydrogen bonds : bond 0.06392 ( 2290) hydrogen bonds : angle 3.38578 ( 6843) covalent geometry : bond 0.00260 (31860) covalent geometry : angle 0.56219 (42867) ********************** 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 529 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 442 time to evaluate : 3.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 94 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8911 (mp) REVERT: R 260 MET cc_start: 0.0360 (mmp) cc_final: -0.0370 (mmp) REVERT: J 90 MET cc_start: 0.9104 (ttm) cc_final: 0.8672 (ttm) REVERT: J 185 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8183 (tm-30) REVERT: J 220 ARG cc_start: 0.8164 (ttm110) cc_final: 0.7841 (ttp80) REVERT: K 36 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7519 (tt) REVERT: K 42 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.6959 (mtm-85) REVERT: K 90 MET cc_start: 0.8460 (mtp) cc_final: 0.8212 (mtt) REVERT: K 202 MET cc_start: 0.8453 (mmm) cc_final: 0.8113 (mmm) REVERT: K 214 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8342 (mt-10) REVERT: K 270 MET cc_start: 0.4166 (tpp) cc_final: 0.3943 (tpp) REVERT: L 38 ASP cc_start: 0.7976 (p0) cc_final: 0.7228 (p0) REVERT: L 42 ARG cc_start: 0.8306 (mmt90) cc_final: 0.7869 (mpt-90) REVERT: L 90 MET cc_start: 0.9291 (mtp) cc_final: 0.8958 (mtp) REVERT: L 101 ASP cc_start: 0.8771 (p0) cc_final: 0.8419 (p0) REVERT: L 126 GLU cc_start: 0.8975 (tt0) cc_final: 0.8621 (tm-30) REVERT: L 135 GLN cc_start: 0.8332 (tp40) cc_final: 0.8113 (tp40) REVERT: N 101 ASP cc_start: 0.8698 (p0) cc_final: 0.8204 (p0) REVERT: N 159 ASN cc_start: 0.9287 (t0) cc_final: 0.8892 (t0) REVERT: O 36 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7290 (tt) REVERT: O 42 ARG cc_start: 0.7951 (ptp90) cc_final: 0.7640 (ptp90) REVERT: O 95 ASP cc_start: 0.9002 (t0) cc_final: 0.8649 (t0) REVERT: O 214 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8027 (mt-10) REVERT: P 188 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7941 (mm-40) REVERT: P 215 GLN cc_start: 0.8795 (tt0) cc_final: 0.8523 (tt0) REVERT: P 221 ARG cc_start: 0.8542 (tpp80) cc_final: 0.8218 (ttm110) REVERT: Q 42 ARG cc_start: 0.8161 (mtt90) cc_final: 0.7770 (mtm-85) REVERT: Q 56 GLU cc_start: 0.8873 (tp30) cc_final: 0.8668 (tp30) REVERT: Q 101 ASP cc_start: 0.8820 (p0) cc_final: 0.8465 (p0) REVERT: Q 185 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8088 (tm-30) REVERT: Q 214 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8296 (tt0) REVERT: Q 221 ARG cc_start: 0.8306 (ttm110) cc_final: 0.7830 (ttm110) REVERT: Q 260 MET cc_start: -0.1983 (mmp) cc_final: -0.2652 (tmm) REVERT: A 3 TYR cc_start: 0.1022 (OUTLIER) cc_final: -0.0107 (p90) REVERT: B 35 MET cc_start: 0.0269 (OUTLIER) cc_final: -0.0849 (tmm) REVERT: B 149 MET cc_start: 0.7930 (mmm) cc_final: 0.7170 (ptt) REVERT: C 1 MET cc_start: 0.4090 (pmm) cc_final: 0.3192 (ppp) REVERT: C 8 MET cc_start: 0.1109 (mmm) cc_final: 0.0714 (mtm) REVERT: C 51 MET cc_start: 0.3500 (mmp) cc_final: 0.2370 (mtm) REVERT: C 111 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8293 (mp10) REVERT: C 148 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.8497 (m-80) REVERT: D 51 MET cc_start: 0.2329 (mmm) cc_final: 0.2128 (tpt) REVERT: D 99 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.7237 (ttt180) REVERT: D 109 ARG cc_start: 0.7748 (tpp80) cc_final: 0.7375 (tpp80) REVERT: D 110 ARG cc_start: 0.7091 (ppt170) cc_final: 0.6874 (ppt170) REVERT: D 111 GLN cc_start: 0.8861 (pp30) cc_final: 0.8567 (pt0) REVERT: D 130 ARG cc_start: 0.8448 (tpm170) cc_final: 0.8146 (tpp-160) REVERT: E 35 MET cc_start: -0.1868 (pmm) cc_final: -0.2178 (ptt) REVERT: E 99 ARG cc_start: 0.7529 (mmm-85) cc_final: 0.6806 (ttt-90) REVERT: E 109 ARG cc_start: 0.7856 (ttm-80) cc_final: 0.7314 (tpp80) REVERT: E 132 ARG cc_start: 0.7940 (tpt90) cc_final: 0.7534 (mmp80) REVERT: E 149 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7513 (tpt) REVERT: F 99 ARG cc_start: 0.7592 (mmm-85) cc_final: 0.6877 (ttt-90) REVERT: F 109 ARG cc_start: 0.7785 (tpp80) cc_final: 0.7577 (tpp80) REVERT: F 132 ARG cc_start: 0.8160 (tpt90) cc_final: 0.7658 (mmp80) REVERT: I 111 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8702 (tp40) REVERT: I 148 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.8277 (m-10) outliers start: 87 outliers final: 72 residues processed: 501 average time/residue: 0.4561 time to fit residues: 351.2194 Evaluate side-chains 519 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 436 time to evaluate : 4.435 ------------------------------------------------------------------------------- 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 229 VAL 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 48 VAL Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 199 SER 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 48 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 229 VAL Chi-restraints excluded: chain L residue 305 LYS Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 212 THR 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 201 SER Chi-restraints excluded: chain O residue 212 THR 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 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 Q residue 229 VAL Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET 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 148 TYR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 82 LEU 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 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 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 111 GLN 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 100 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 264 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 chunk 306 optimal weight: 3.9990 chunk 223 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN J 106 GLN D 121 GLN ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.210174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118429 restraints weight = 49074.966| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.83 r_work: 0.3105 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 31860 Z= 0.159 Angle : 0.678 59.161 42867 Z= 0.373 Chirality : 0.037 0.640 4635 Planarity : 0.003 0.053 5985 Dihedral : 3.596 38.452 4581 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.11 % Favored : 93.64 % Rotamer: Outliers : 2.89 % Allowed : 29.92 % Favored : 67.19 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.14), residues: 4122 helix: 3.08 (0.10), residues: 2970 sheet: None (None), residues: 0 loop : -3.19 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 77 HIS 0.001 0.000 HIS O 198 PHE 0.031 0.001 PHE E 112 TYR 0.011 0.001 TYR L 62 ARG 0.011 0.000 ARG G 109 Details of bonding type rmsd hydrogen bonds : bond 0.06492 ( 2290) hydrogen bonds : angle 3.39905 ( 6843) covalent geometry : bond 0.00326 (31860) covalent geometry : angle 0.67783 (42867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20666.96 seconds wall clock time: 356 minutes 18.60 seconds (21378.60 seconds total)