Starting phenix.real_space_refine on Fri Jun 27 04:50:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vxq_43629/06_2025/8vxq_43629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vxq_43629/06_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_43629/06_2025/8vxq_43629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vxq_43629/06_2025/8vxq_43629.map" model { file = "/net/cci-nas-00/data/ceres_data/8vxq_43629/06_2025/8vxq_43629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vxq_43629/06_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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 18.55, per 1000 atoms: 0.59 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: 8.96 Conformation dependent library (CDL) restraints added in 4.6 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: 2.74 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: 10.16 Time building geometry restraints manager: 10.42 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: 0.03 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: 5.980 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: 1.470 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 69.440 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.310 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: 0.020 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.110 ------------------------------------------------------------------------------- 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 : 3.289 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: 0.4505 time to fit residues: 306.7456 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 : 3.294 ------------------------------------------------------------------------------- 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 = 0.122785 restraints weight = 49195.643| |-----------------------------------------------------------------------------| 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 6.616 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 3.56877 ( 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 : 3.241 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: 0.8645 (tm-30) cc_final: 0.8428 (tm-30) REVERT: K 42 ARG cc_start: 0.7760 (mtt-85) cc_final: 0.7510 (mtm-85) REVERT: L 90 MET cc_start: 0.9051 (mtp) cc_final: 0.8810 (mtp) REVERT: L 95 ASP cc_start: 0.8741 (t70) cc_final: 0.8223 (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: 0.8033 (mtt90) cc_final: 0.7809 (mtm-85) REVERT: Q 101 ASP cc_start: 0.8496 (p0) cc_final: 0.8060 (p0) REVERT: Q 126 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7807 (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: 0.6431 (mpt) REVERT: B 99 ARG cc_start: 0.7055 (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: 0.8185 (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: 0.6895 (ttt-90) REVERT: F 102 ARG cc_start: 0.8292 (ttm170) cc_final: 0.7969 (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: 0.4626 time to fit residues: 350.6214 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 : 3.263 ------------------------------------------------------------------------------- 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: 9.9990 chunk 365 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 399 optimal weight: 8.9990 chunk 235 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 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: 0.0070 overall best weight: 2.1804 ------------------------------------------------------------------------------- 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 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 = 0.4435 r_free = 0.4435 target = 0.205260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110009 restraints weight = 49259.724| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.81 r_work: 0.2987 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 31860 Z= 0.309 Angle : 0.644 9.194 42867 Z= 0.350 Chirality : 0.040 0.171 4635 Planarity : 0.004 0.133 5985 Dihedral : 3.988 51.590 4587 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.77 % Favored : 93.04 % Rotamer: Outliers : 4.10 % Allowed : 27.34 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.14), residues: 4122 helix: 2.68 (0.10), residues: 2979 sheet: None (None), residues: 0 loop : -3.26 (0.15), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP A 77 HIS 0.003 0.001 HIS P 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 0.07863 ( 2290) hydrogen bonds : angle 3.97689 ( 6843) covalent geometry : bond 0.00707 (31860) covalent geometry : angle 0.64393 (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 555 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 423 time to evaluate : 3.386 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: R 95 ASP cc_start: 0.8462 (t70) cc_final: 0.8162 (t0) REVERT: R 101 ASP cc_start: 0.8975 (p0) cc_final: 0.8759 (p0) REVERT: R 107 ILE cc_start: 0.8498 (pt) cc_final: 0.8239 (mt) REVERT: R 219 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8585 (tt) REVERT: R 260 MET cc_start: -0.0512 (mmp) cc_final: -0.1308 (mmp) REVERT: J 90 MET cc_start: 0.9337 (ttm) cc_final: 0.9072 (ttm) REVERT: J 126 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8288 (tm-30) REVERT: J 217 ASP cc_start: 0.8738 (t0) cc_final: 0.8153 (t0) REVERT: J 220 ARG cc_start: 0.8185 (ttm110) cc_final: 0.7789 (ttp80) REVERT: K 202 MET cc_start: 0.8657 (mmm) cc_final: 0.8379 (mmm) REVERT: L 90 MET cc_start: 0.9401 (mtp) cc_final: 0.9026 (mtp) REVERT: N 101 ASP cc_start: 0.8925 (p0) cc_final: 0.8456 (p0) REVERT: O 176 ASN cc_start: 0.8569 (t0) cc_final: 0.8312 (m110) REVERT: O 221 ARG cc_start: 0.8448 (ttm-80) cc_final: 0.8150 (ttm110) REVERT: P 101 ASP cc_start: 0.8899 (p0) cc_final: 0.8605 (p0) REVERT: P 215 GLN cc_start: 0.8669 (tt0) cc_final: 0.8310 (tt0) REVERT: Q 56 GLU cc_start: 0.8917 (tp30) cc_final: 0.8647 (tp30) REVERT: Q 58 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8454 (t160) REVERT: Q 185 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8070 (tm-30) REVERT: Q 221 ARG cc_start: 0.8321 (ttm110) cc_final: 0.7798 (ttm110) REVERT: Q 260 MET cc_start: -0.2548 (mmp) cc_final: -0.3292 (tmm) REVERT: A 3 TYR cc_start: 0.0914 (OUTLIER) cc_final: -0.0014 (p90) REVERT: B 99 ARG cc_start: 0.7258 (mmm-85) cc_final: 0.6731 (tpp-160) REVERT: B 110 ARG cc_start: 0.7011 (ttt-90) cc_final: 0.6647 (ttp80) REVERT: B 148 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: C 1 MET cc_start: 0.3907 (pmm) cc_final: 0.1581 (tpt) REVERT: C 8 MET cc_start: 0.1127 (mmm) cc_final: 0.0746 (mtm) REVERT: C 33 MET cc_start: 0.1127 (ttp) cc_final: 0.0639 (ttp) REVERT: C 51 MET cc_start: 0.3014 (mmp) cc_final: 0.1370 (mtt) REVERT: D 51 MET cc_start: 0.1700 (mmm) cc_final: 0.1375 (tpp) REVERT: D 121 GLN cc_start: 0.7972 (tt0) cc_final: 0.7745 (tm-30) REVERT: E 14 LEU cc_start: 0.3808 (OUTLIER) cc_final: 0.3606 (pt) REVERT: E 98 GLN cc_start: 0.8389 (tt0) cc_final: 0.8178 (tp40) REVERT: F 98 GLN cc_start: 0.7953 (tt0) cc_final: 0.7740 (tp40) REVERT: F 99 ARG cc_start: 0.7517 (mmm-85) cc_final: 0.6716 (ttt-90) REVERT: F 114 MET cc_start: 0.8657 (tmm) cc_final: 0.8409 (tmm) REVERT: F 132 ARG cc_start: 0.8141 (tpt90) cc_final: 0.7628 (mmp80) REVERT: F 149 MET cc_start: 0.8899 (tpt) cc_final: 0.8218 (ptt) REVERT: H 77 TRP cc_start: 0.7858 (p90) cc_final: 0.7565 (p90) outliers start: 132 outliers final: 76 residues processed: 524 average time/residue: 0.4523 time to fit residues: 371.0274 Evaluate side-chains 503 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 422 time to evaluate : 3.588 ------------------------------------------------------------------------------- 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 219 LEU 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 199 SER 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 199 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 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 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 199 SER 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 D residue 127 LEU Chi-restraints excluded: chain E residue 14 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 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: 8.9990 chunk 100 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 363 optimal weight: 30.0000 chunk 114 optimal weight: 0.9980 chunk 374 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 404 optimal weight: 0.9980 chunk 311 optimal weight: 5.9990 chunk 274 optimal weight: 30.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 176 ASN K 176 ASN M 176 ASN N 176 ASN P 156 GLN P 238 GLN Q 58 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN E 111 GLN F 111 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.209249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.115642 restraints weight = 48900.216| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.87 r_work: 0.3069 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31860 Z= 0.156 Angle : 0.528 7.726 42867 Z= 0.282 Chirality : 0.035 0.157 4635 Planarity : 0.003 0.106 5985 Dihedral : 3.750 49.334 4585 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.11 % Favored : 93.69 % Rotamer: Outliers : 3.17 % Allowed : 27.87 % Favored : 68.96 % 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: 1.97 (0.14), residues: 4122 helix: 2.90 (0.10), residues: 2979 sheet: -2.77 (0.56), residues: 90 loop : -3.43 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 77 HIS 0.001 0.000 HIS J 198 PHE 0.036 0.001 PHE O 211 TYR 0.016 0.001 TYR G 116 ARG 0.009 0.000 ARG L 216 Details of bonding type rmsd hydrogen bonds : bond 0.06883 ( 2290) hydrogen bonds : angle 3.60467 ( 6843) covalent geometry : bond 0.00327 (31860) covalent geometry : angle 0.52788 (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 537 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 435 time to evaluate : 7.493 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 72 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8511 (tm-30) REVERT: R 95 ASP cc_start: 0.8296 (t70) cc_final: 0.7971 (t70) REVERT: R 260 MET cc_start: -0.0326 (mmp) cc_final: -0.1032 (mmp) REVERT: J 42 ARG cc_start: 0.7755 (ptp90) cc_final: 0.7539 (ptp90) REVERT: J 90 MET cc_start: 0.9298 (ttm) cc_final: 0.9054 (ttm) REVERT: J 217 ASP cc_start: 0.8687 (t0) cc_final: 0.8172 (t0) REVERT: J 220 ARG cc_start: 0.8162 (ttm110) cc_final: 0.7810 (ttp80) REVERT: K 36 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7522 (tt) REVERT: K 42 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7428 (mtm-85) REVERT: L 90 MET cc_start: 0.9249 (mtp) cc_final: 0.8944 (mtp) REVERT: L 135 GLN cc_start: 0.8361 (tp40) cc_final: 0.8135 (tp40) REVERT: N 101 ASP cc_start: 0.8848 (p0) cc_final: 0.8486 (p0) REVERT: O 36 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7140 (tt) REVERT: O 159 ASN cc_start: 0.9169 (OUTLIER) cc_final: 0.8791 (t0) REVERT: O 214 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7904 (mt-10) REVERT: O 221 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.8186 (ttm110) REVERT: P 101 ASP cc_start: 0.8794 (p0) cc_final: 0.8546 (p0) REVERT: P 188 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7977 (mm-40) REVERT: P 215 GLN cc_start: 0.8694 (tt0) cc_final: 0.8341 (tt0) REVERT: Q 42 ARG cc_start: 0.8165 (mtt90) cc_final: 0.7816 (mtt90) REVERT: Q 58 ASN cc_start: 0.8632 (OUTLIER) cc_final: 0.7911 (t0) REVERT: Q 90 MET cc_start: 0.9161 (mtp) cc_final: 0.8922 (mtt) REVERT: Q 101 ASP cc_start: 0.8656 (p0) cc_final: 0.8445 (p0) REVERT: Q 185 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8104 (tm-30) REVERT: Q 214 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8215 (tt0) REVERT: Q 221 ARG cc_start: 0.8325 (ttm110) cc_final: 0.7581 (ttm110) REVERT: Q 260 MET cc_start: -0.2426 (mmp) cc_final: -0.3038 (tmm) REVERT: A 3 TYR cc_start: 0.1127 (OUTLIER) cc_final: 0.0040 (p90) REVERT: B 99 ARG cc_start: 0.7260 (mmm-85) cc_final: 0.6719 (tpp-160) REVERT: B 104 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7444 (tm-30) REVERT: B 110 ARG cc_start: 0.6876 (ttt-90) cc_final: 0.6446 (ttp80) REVERT: B 148 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.8015 (m-80) REVERT: B 149 MET cc_start: 0.7849 (mmm) cc_final: 0.7272 (ptt) REVERT: B 152 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7863 (p0) REVERT: C 1 MET cc_start: 0.4010 (pmm) cc_final: 0.1926 (tpt) REVERT: C 8 MET cc_start: 0.1127 (mmm) cc_final: 0.0744 (mtm) REVERT: C 33 MET cc_start: 0.1100 (ttp) cc_final: 0.0562 (ttp) REVERT: C 51 MET cc_start: 0.2879 (mmp) cc_final: 0.1181 (mtt) REVERT: C 111 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8323 (mp10) REVERT: D 51 MET cc_start: 0.1927 (mmm) cc_final: 0.1371 (tpp) REVERT: D 111 GLN cc_start: 0.8628 (pp30) cc_final: 0.8290 (pt0) REVERT: D 121 GLN cc_start: 0.8050 (tt0) cc_final: 0.7817 (tm-30) REVERT: E 35 MET cc_start: -0.1760 (pmm) cc_final: -0.2024 (ptt) REVERT: E 98 GLN cc_start: 0.8371 (tt0) cc_final: 0.8163 (tp40) REVERT: E 149 MET cc_start: 0.7830 (mmp) cc_final: 0.7480 (tpt) REVERT: F 99 ARG cc_start: 0.7503 (mmm-85) cc_final: 0.6700 (ttt-90) REVERT: F 114 MET cc_start: 0.8645 (tmm) cc_final: 0.8419 (tmm) REVERT: F 132 ARG cc_start: 0.8103 (tpt90) cc_final: 0.7695 (mmp80) REVERT: H 149 MET cc_start: 0.7960 (ttp) cc_final: 0.7579 (ptt) outliers start: 102 outliers final: 59 residues processed: 514 average time/residue: 0.6639 time to fit residues: 543.3582 Evaluate side-chains 486 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 418 time to evaluate : 4.291 ------------------------------------------------------------------------------- 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 81 SER Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain R residue 305 LYS Chi-restraints excluded: chain J residue 40 ILE 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 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 L residue 66 VAL Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain 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 Q residue 53 LEU Chi-restraints excluded: chain Q residue 58 ASN 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 A residue 3 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 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 E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 261 optimal weight: 3.9990 chunk 390 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 306 optimal weight: 2.9990 chunk 373 optimal weight: 10.0000 chunk 28 optimal weight: 0.2980 chunk 323 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 265 optimal weight: 7.9990 chunk 341 optimal weight: 0.7980 chunk 257 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN M 176 ASN N 176 ASN O 176 ASN Q 30 GLN Q 58 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN F 111 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.208123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.114521 restraints weight = 48578.879| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.79 r_work: 0.3047 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31860 Z= 0.185 Angle : 0.546 9.807 42867 Z= 0.291 Chirality : 0.036 0.157 4635 Planarity : 0.003 0.082 5985 Dihedral : 3.723 48.609 4585 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.45 % Favored : 93.30 % Rotamer: Outliers : 3.72 % Allowed : 27.68 % Favored : 68.59 % 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: 1.97 (0.14), residues: 4122 helix: 2.90 (0.10), residues: 2979 sheet: -2.83 (0.55), residues: 90 loop : -3.41 (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 R 198 PHE 0.027 0.001 PHE E 112 TYR 0.016 0.001 TYR G 116 ARG 0.006 0.000 ARG N 221 Details of bonding type rmsd hydrogen bonds : bond 0.07024 ( 2290) hydrogen bonds : angle 3.61251 ( 6843) covalent geometry : bond 0.00411 (31860) covalent geometry : angle 0.54564 (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 540 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 420 time to evaluate : 3.778 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 95 ASP cc_start: 0.8266 (t70) cc_final: 0.7903 (t70) REVERT: R 260 MET cc_start: -0.0065 (mmp) cc_final: -0.0632 (mmp) REVERT: R 305 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.7204 (ptpp) REVERT: J 90 MET cc_start: 0.9261 (ttm) cc_final: 0.9058 (ttm) REVERT: J 217 ASP cc_start: 0.8763 (t0) cc_final: 0.8308 (t0) REVERT: J 220 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7785 (ttp80) REVERT: K 36 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7533 (tt) REVERT: K 90 MET cc_start: 0.8654 (mtp) cc_final: 0.8357 (mtt) REVERT: K 202 MET cc_start: 0.8508 (mmm) cc_final: 0.8151 (mmm) REVERT: L 90 MET cc_start: 0.9410 (mtp) cc_final: 0.9114 (mtp) REVERT: L 135 GLN cc_start: 0.8364 (tp40) cc_final: 0.8137 (tp40) REVERT: L 221 ARG cc_start: 0.8139 (ttm110) cc_final: 0.7858 (ttm110) REVERT: L 260 MET cc_start: 0.0808 (mmp) cc_final: -0.1670 (tmm) REVERT: N 101 ASP cc_start: 0.8843 (p0) cc_final: 0.8485 (p0) REVERT: N 126 GLU cc_start: 0.8852 (tt0) cc_final: 0.8552 (tm-30) REVERT: O 36 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7151 (tt) REVERT: O 95 ASP cc_start: 0.9018 (t0) cc_final: 0.8813 (t0) REVERT: O 214 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7862 (mt-10) REVERT: O 221 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8194 (ttm110) REVERT: P 101 ASP cc_start: 0.8836 (p0) cc_final: 0.8611 (p0) REVERT: P 188 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7982 (mm-40) REVERT: P 215 GLN cc_start: 0.8700 (tt0) cc_final: 0.8355 (tt0) REVERT: Q 56 GLU cc_start: 0.8829 (tp30) cc_final: 0.8558 (tp30) REVERT: Q 58 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.7778 (t0) REVERT: Q 90 MET cc_start: 0.9293 (mtp) cc_final: 0.8816 (mtp) REVERT: Q 101 ASP cc_start: 0.8713 (p0) cc_final: 0.8436 (p0) REVERT: Q 185 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8092 (tm-30) REVERT: Q 214 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8236 (tt0) REVERT: Q 221 ARG cc_start: 0.8272 (ttm110) cc_final: 0.7594 (ttm110) REVERT: Q 260 MET cc_start: -0.2390 (mmp) cc_final: -0.3006 (tmm) REVERT: A 3 TYR cc_start: 0.1325 (OUTLIER) cc_final: 0.0259 (p90) REVERT: B 104 GLN cc_start: 0.7710 (tm-30) cc_final: 0.7466 (tm-30) REVERT: B 111 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8106 (pp30) REVERT: B 152 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7977 (p0) REVERT: C 1 MET cc_start: 0.3948 (pmm) cc_final: 0.2991 (ppp) REVERT: C 8 MET cc_start: 0.1134 (mmm) cc_final: 0.0749 (mtm) REVERT: C 33 MET cc_start: 0.1371 (ttp) cc_final: 0.1067 (ttp) REVERT: C 51 MET cc_start: 0.2853 (mmp) cc_final: 0.1164 (mtt) REVERT: C 111 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8297 (mp10) REVERT: D 51 MET cc_start: 0.2091 (mmm) cc_final: 0.1516 (tpp) REVERT: E 35 MET cc_start: -0.1751 (pmm) cc_final: -0.2017 (ptt) REVERT: E 149 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7557 (tpt) REVERT: F 99 ARG cc_start: 0.7494 (mmm-85) cc_final: 0.6745 (ttt-90) REVERT: F 114 MET cc_start: 0.8695 (tmm) cc_final: 0.8482 (tmm) REVERT: F 132 ARG cc_start: 0.8038 (tpt90) cc_final: 0.7637 (mmp80) REVERT: H 149 MET cc_start: 0.7959 (ttp) cc_final: 0.7649 (ptt) outliers start: 120 outliers final: 79 residues processed: 515 average time/residue: 0.4371 time to fit residues: 354.4469 Evaluate side-chains 507 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 418 time to evaluate : 3.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain R residue 305 LYS Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 199 SER 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 124 GLN Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 105 LYS 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 94 LEU 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 N residue 251 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 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 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 201 SER Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 58 ASN 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 A residue 3 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 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 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 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 149 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 3 TYR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 235 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 175 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 302 optimal weight: 0.0070 chunk 330 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 193 optimal weight: 0.9980 chunk 310 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN M 156 GLN M 176 ASN N 176 ASN O 176 ASN Q 58 ASN B 152 ASN D 121 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 = 0.4480 r_free = 0.4480 target = 0.213779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118825 restraints weight = 48553.591| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.97 r_work: 0.3086 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31860 Z= 0.139 Angle : 0.522 9.593 42867 Z= 0.275 Chirality : 0.035 0.157 4635 Planarity : 0.003 0.070 5985 Dihedral : 3.620 47.001 4585 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.28 % Favored : 93.47 % Rotamer: Outliers : 3.35 % Allowed : 28.00 % Favored : 68.65 % 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: 2.13 (0.14), residues: 4122 helix: 3.05 (0.10), residues: 2970 sheet: -2.83 (0.55), residues: 90 loop : -3.39 (0.16), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 77 HIS 0.001 0.000 HIS L 198 PHE 0.027 0.001 PHE E 112 TYR 0.012 0.001 TYR G 116 ARG 0.009 0.000 ARG J 42 Details of bonding type rmsd hydrogen bonds : bond 0.06516 ( 2290) hydrogen bonds : angle 3.45316 ( 6843) covalent geometry : bond 0.00276 (31860) covalent geometry : angle 0.52234 (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 548 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 440 time to evaluate : 3.581 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 95 ASP cc_start: 0.8251 (t70) cc_final: 0.7794 (t70) REVERT: R 260 MET cc_start: -0.0215 (mmp) cc_final: -0.0765 (mmp) REVERT: J 42 ARG cc_start: 0.7666 (ptp90) cc_final: 0.7456 (ptp90) REVERT: J 185 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8182 (tm-30) REVERT: J 217 ASP cc_start: 0.8734 (t0) cc_final: 0.8281 (t0) REVERT: J 220 ARG cc_start: 0.8149 (ttm110) cc_final: 0.7787 (ttp80) REVERT: K 36 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7593 (tt) REVERT: K 90 MET cc_start: 0.8549 (mtp) cc_final: 0.8253 (mtt) REVERT: L 90 MET cc_start: 0.9300 (mtp) cc_final: 0.9030 (mtp) REVERT: L 101 ASP cc_start: 0.8875 (p0) cc_final: 0.8512 (p0) REVERT: L 124 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8752 (mt0) REVERT: L 126 GLU cc_start: 0.8989 (tt0) cc_final: 0.8675 (tm-30) REVERT: L 135 GLN cc_start: 0.8362 (tp40) cc_final: 0.8107 (tp40) REVERT: L 260 MET cc_start: 0.0845 (mmp) cc_final: -0.1670 (tmm) REVERT: M 228 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7488 (pp) REVERT: N 42 ARG cc_start: 0.8526 (mmm-85) cc_final: 0.8224 (mmm160) REVERT: N 101 ASP cc_start: 0.8779 (p0) cc_final: 0.8450 (p0) REVERT: N 159 ASN cc_start: 0.9310 (t0) cc_final: 0.8949 (t0) REVERT: O 36 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7127 (tt) REVERT: O 159 ASN cc_start: 0.9069 (OUTLIER) cc_final: 0.8703 (t0) REVERT: O 214 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7882 (mt-10) REVERT: O 221 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8178 (ttm110) REVERT: P 101 ASP cc_start: 0.8818 (p0) cc_final: 0.8609 (p0) REVERT: P 188 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7968 (mm-40) REVERT: P 215 GLN cc_start: 0.8704 (tt0) cc_final: 0.8321 (tt0) REVERT: Q 42 ARG cc_start: 0.8120 (mtt90) cc_final: 0.7812 (mtt90) REVERT: Q 101 ASP cc_start: 0.8718 (p0) cc_final: 0.8434 (p0) REVERT: Q 185 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8068 (tm-30) REVERT: Q 214 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8239 (tt0) REVERT: Q 221 ARG cc_start: 0.8288 (ttm110) cc_final: 0.7648 (ttm110) REVERT: Q 260 MET cc_start: -0.2440 (mmp) cc_final: -0.3024 (tmm) REVERT: A 3 TYR cc_start: 0.1110 (OUTLIER) cc_final: 0.0051 (p90) REVERT: B 35 MET cc_start: 0.0125 (OUTLIER) cc_final: -0.1024 (tmm) REVERT: B 99 ARG cc_start: 0.7262 (mmm-85) cc_final: 0.6726 (tpp-160) REVERT: B 104 GLN cc_start: 0.7711 (tm-30) cc_final: 0.7450 (tm-30) REVERT: B 110 ARG cc_start: 0.7044 (ttt-90) cc_final: 0.6433 (ttp80) REVERT: B 111 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8054 (pp30) REVERT: B 149 MET cc_start: 0.7835 (mmm) cc_final: 0.7356 (ptt) REVERT: C 1 MET cc_start: 0.4082 (pmm) cc_final: 0.3181 (ppp) REVERT: C 8 MET cc_start: 0.1133 (mmm) cc_final: 0.0747 (mtm) REVERT: C 33 MET cc_start: 0.1321 (ttp) cc_final: 0.0995 (ttp) REVERT: C 51 MET cc_start: 0.2825 (mmp) cc_final: 0.1158 (mtt) REVERT: C 111 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8287 (mp10) REVERT: D 51 MET cc_start: 0.2164 (mmm) cc_final: 0.1556 (tpp) REVERT: D 111 GLN cc_start: 0.8604 (pp30) cc_final: 0.8255 (pt0) REVERT: E 35 MET cc_start: -0.1751 (pmm) cc_final: -0.2015 (ptt) REVERT: E 99 ARG cc_start: 0.7392 (mmm-85) cc_final: 0.6590 (ttt-90) REVERT: E 109 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7425 (tpp80) REVERT: E 110 ARG cc_start: 0.7356 (ttt-90) cc_final: 0.7145 (tmt170) REVERT: E 132 ARG cc_start: 0.7821 (tpt90) cc_final: 0.7490 (mmp80) REVERT: E 149 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7554 (tpt) REVERT: F 99 ARG cc_start: 0.7482 (mmm-85) cc_final: 0.6752 (ttt-90) REVERT: F 132 ARG cc_start: 0.8102 (tpt90) cc_final: 0.7702 (mmp80) outliers start: 108 outliers final: 69 residues processed: 518 average time/residue: 0.4492 time to fit residues: 360.4194 Evaluate side-chains 499 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 419 time to evaluate : 3.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 81 SER Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain R residue 305 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 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 L residue 66 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 228 LEU Chi-restraints excluded: chain M residue 270 MET 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 139 LEU Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain 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 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 216 ARG Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 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 D residue 40 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 149 MET Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 67 VAL 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 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: 1.9990 chunk 397 optimal weight: 1.9990 chunk 361 optimal weight: 30.0000 chunk 401 optimal weight: 8.9990 chunk 294 optimal weight: 9.9990 chunk 270 optimal weight: 7.9990 chunk 28 optimal weight: 0.2980 chunk 384 optimal weight: 6.9990 chunk 377 optimal weight: 2.9990 chunk 341 optimal weight: 0.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN J 30 GLN K 238 GLN M 176 ASN E 111 GLN F 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.207638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.112588 restraints weight = 49060.998| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.82 r_work: 0.3018 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 31860 Z= 0.216 Angle : 0.585 10.222 42867 Z= 0.310 Chirality : 0.037 0.158 4635 Planarity : 0.003 0.067 5985 Dihedral : 3.736 46.836 4583 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.45 % Favored : 93.30 % Rotamer: Outliers : 3.79 % Allowed : 27.90 % Favored : 68.31 % 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: 1.96 (0.14), residues: 4122 helix: 2.88 (0.10), residues: 2979 sheet: -2.96 (0.54), residues: 90 loop : -3.38 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 77 HIS 0.001 0.001 HIS J 198 PHE 0.031 0.001 PHE A 112 TYR 0.010 0.001 TYR E 116 ARG 0.009 0.000 ARG F 109 Details of bonding type rmsd hydrogen bonds : bond 0.07256 ( 2290) hydrogen bonds : angle 3.65706 ( 6843) covalent geometry : bond 0.00487 (31860) covalent geometry : angle 0.58469 (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 556 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 434 time to evaluate : 3.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 260 MET cc_start: 0.0173 (mmp) cc_final: -0.0546 (mmp) REVERT: J 90 MET cc_start: 0.9177 (ttm) cc_final: 0.8719 (ttm) REVERT: J 217 ASP cc_start: 0.8798 (t0) cc_final: 0.8288 (t0) REVERT: J 220 ARG cc_start: 0.8205 (ttm110) cc_final: 0.7826 (ttp80) REVERT: K 36 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7593 (tt) REVERT: K 90 MET cc_start: 0.8557 (mtp) cc_final: 0.8260 (mtt) REVERT: K 202 MET cc_start: 0.8582 (mmm) cc_final: 0.8209 (mmm) REVERT: L 90 MET cc_start: 0.9411 (mtp) cc_final: 0.9018 (mtp) REVERT: L 101 ASP cc_start: 0.8943 (p0) cc_final: 0.8566 (p0) REVERT: L 135 GLN cc_start: 0.8384 (tp40) cc_final: 0.8148 (tp40) REVERT: L 221 ARG cc_start: 0.8174 (ttm110) cc_final: 0.7923 (ttm110) REVERT: L 260 MET cc_start: 0.0306 (mmp) cc_final: -0.1940 (tmm) REVERT: N 95 ASP cc_start: 0.8878 (t70) cc_final: 0.8326 (t70) REVERT: N 101 ASP cc_start: 0.8862 (p0) cc_final: 0.8528 (p0) REVERT: N 119 LYS cc_start: 0.8796 (mtpt) cc_final: 0.8573 (ttmm) REVERT: O 36 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7176 (tt) REVERT: O 214 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7918 (mt-10) REVERT: P 101 ASP cc_start: 0.8854 (p0) cc_final: 0.8649 (p0) REVERT: P 188 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8004 (mm-40) REVERT: P 215 GLN cc_start: 0.8708 (tt0) cc_final: 0.8336 (tt0) REVERT: Q 42 ARG cc_start: 0.8279 (mtt90) cc_final: 0.7871 (mpt-90) REVERT: Q 58 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8240 (t0) REVERT: Q 101 ASP cc_start: 0.8762 (p0) cc_final: 0.8458 (p0) REVERT: Q 185 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8080 (tm-30) REVERT: Q 214 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8277 (tt0) REVERT: Q 221 ARG cc_start: 0.8302 (ttm110) cc_final: 0.7628 (ttm110) REVERT: Q 260 MET cc_start: -0.2366 (mmp) cc_final: -0.2963 (tmm) REVERT: A 3 TYR cc_start: 0.1372 (OUTLIER) cc_final: 0.0271 (p90) REVERT: B 35 MET cc_start: 0.0175 (OUTLIER) cc_final: -0.0989 (tmm) REVERT: B 104 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7534 (tm-30) REVERT: B 111 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8066 (pp30) REVERT: B 149 MET cc_start: 0.7887 (mmm) cc_final: 0.7277 (ptt) REVERT: C 1 MET cc_start: 0.4005 (pmm) cc_final: 0.3070 (ppp) REVERT: C 33 MET cc_start: 0.1523 (ttp) cc_final: 0.1172 (ttp) REVERT: C 51 MET cc_start: 0.3042 (mmp) cc_final: 0.1527 (mtm) REVERT: C 111 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8281 (mp10) REVERT: D 51 MET cc_start: 0.2190 (mmm) cc_final: 0.1948 (tpt) REVERT: D 121 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: E 35 MET cc_start: -0.1740 (pmm) cc_final: -0.2081 (ptt) REVERT: E 99 ARG cc_start: 0.7479 (mmm-85) cc_final: 0.6742 (ttt-90) REVERT: E 109 ARG cc_start: 0.8003 (ttm-80) cc_final: 0.7435 (tpp80) REVERT: E 110 ARG cc_start: 0.7330 (ttt-90) cc_final: 0.6998 (tmt170) REVERT: E 132 ARG cc_start: 0.7877 (tpt90) cc_final: 0.7515 (mmp80) REVERT: E 149 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7497 (tpt) REVERT: F 99 ARG cc_start: 0.7522 (mmm-85) cc_final: 0.6760 (ttt-90) REVERT: F 132 ARG cc_start: 0.7958 (tpt90) cc_final: 0.7538 (mmp80) REVERT: H 111 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8104 (mp10) REVERT: I 148 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.8337 (m-10) outliers start: 122 outliers final: 93 residues processed: 525 average time/residue: 0.4308 time to fit residues: 354.2841 Evaluate side-chains 532 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 427 time to evaluate : 3.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 81 SER Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 305 LYS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 170 VAL 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 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 238 GLN Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain M residue 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 270 MET Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 139 LEU 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 303 VAL Chi-restraints excluded: chain O residue 36 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 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 212 THR 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 58 ASN 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 216 ARG 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 A residue 79 LEU 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 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 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 F residue 74 THR Chi-restraints excluded: chain F residue 79 LEU 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 74 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 193 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 125 optimal weight: 0.2980 chunk 397 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 337 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 chunk 232 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN J 176 ASN K 176 ASN K 238 GLN M 176 ASN N 176 ASN O 176 ASN P 176 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 = 0.4477 r_free = 0.4477 target = 0.214193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.119288 restraints weight = 49089.887| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.00 r_work: 0.3066 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31860 Z= 0.147 Angle : 0.550 9.663 42867 Z= 0.287 Chirality : 0.035 0.158 4635 Planarity : 0.003 0.057 5985 Dihedral : 3.617 44.895 4583 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.07 % Favored : 93.69 % Rotamer: Outliers : 3.57 % Allowed : 28.21 % Favored : 68.22 % 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: 2.23 (0.14), residues: 4122 helix: 3.10 (0.10), residues: 2934 sheet: None (None), residues: 0 loop : -3.10 (0.15), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 77 HIS 0.000 0.000 HIS L 198 PHE 0.029 0.001 PHE A 112 TYR 0.010 0.001 TYR L 62 ARG 0.010 0.000 ARG N 220 Details of bonding type rmsd hydrogen bonds : bond 0.06594 ( 2290) hydrogen bonds : angle 3.45997 ( 6843) covalent geometry : bond 0.00303 (31860) covalent geometry : angle 0.54976 (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 549 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 434 time to evaluate : 3.521 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 95 ASP cc_start: 0.8232 (t70) cc_final: 0.7727 (t70) REVERT: R 126 GLU cc_start: 0.8928 (tt0) cc_final: 0.8643 (tm-30) REVERT: R 260 MET cc_start: 0.0089 (mmp) cc_final: -0.0599 (mmp) REVERT: J 90 MET cc_start: 0.9132 (ttm) cc_final: 0.8728 (ttm) REVERT: J 185 GLN cc_start: 0.8409 (tm-30) cc_final: 0.8177 (tm-30) REVERT: J 217 ASP cc_start: 0.8726 (t0) cc_final: 0.8275 (t0) REVERT: J 220 ARG cc_start: 0.8157 (ttm110) cc_final: 0.7791 (ttp80) REVERT: K 36 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7471 (tt) REVERT: K 90 MET cc_start: 0.8502 (mtp) cc_final: 0.8224 (mtt) REVERT: L 38 ASP cc_start: 0.8122 (p0) cc_final: 0.7453 (t70) REVERT: L 90 MET cc_start: 0.9364 (mtp) cc_final: 0.9032 (mtp) REVERT: L 101 ASP cc_start: 0.8869 (p0) cc_final: 0.8427 (p0) REVERT: L 126 GLU cc_start: 0.8979 (tt0) cc_final: 0.8636 (tm-30) REVERT: L 135 GLN cc_start: 0.8357 (tp40) cc_final: 0.8085 (tp40) REVERT: L 260 MET cc_start: 0.0322 (mmp) cc_final: -0.1962 (tmm) REVERT: N 95 ASP cc_start: 0.8772 (t70) cc_final: 0.8205 (t70) REVERT: N 101 ASP cc_start: 0.8818 (p0) cc_final: 0.8515 (p0) REVERT: N 119 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8503 (ttmm) REVERT: N 159 ASN cc_start: 0.9315 (t0) cc_final: 0.8951 (t0) REVERT: N 214 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8087 (mt-10) REVERT: O 36 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7156 (tt) REVERT: O 42 ARG cc_start: 0.7914 (ptp90) cc_final: 0.7668 (ptp90) REVERT: O 159 ASN cc_start: 0.9096 (OUTLIER) cc_final: 0.8723 (t0) REVERT: O 214 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7915 (mt-10) REVERT: P 188 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7975 (mm-40) REVERT: Q 42 ARG cc_start: 0.8156 (mtt90) cc_final: 0.7726 (mpt-90) REVERT: Q 58 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.7869 (t0) REVERT: Q 90 MET cc_start: 0.9263 (mtp) cc_final: 0.9005 (mtp) REVERT: Q 101 ASP cc_start: 0.8758 (p0) cc_final: 0.8461 (p0) REVERT: Q 185 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8092 (tm-30) REVERT: Q 214 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8294 (tt0) REVERT: Q 221 ARG cc_start: 0.8332 (ttm110) cc_final: 0.7674 (ttm110) REVERT: Q 260 MET cc_start: -0.2422 (mmp) cc_final: -0.2993 (tmm) REVERT: A 3 TYR cc_start: 0.0932 (OUTLIER) cc_final: -0.0154 (p90) REVERT: B 35 MET cc_start: 0.0183 (OUTLIER) cc_final: -0.0972 (tmm) REVERT: B 104 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7705 (tm-30) REVERT: C 1 MET cc_start: 0.4009 (pmm) cc_final: 0.3080 (ppp) REVERT: C 33 MET cc_start: 0.1482 (ttp) cc_final: 0.1124 (ttp) REVERT: C 51 MET cc_start: 0.2973 (mmp) cc_final: 0.1571 (mtm) REVERT: C 111 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8258 (mp10) REVERT: D 51 MET cc_start: 0.2333 (mmm) cc_final: 0.2100 (tpt) REVERT: D 111 GLN cc_start: 0.8686 (pp30) cc_final: 0.8303 (pt0) REVERT: E 35 MET cc_start: -0.1880 (pmm) cc_final: -0.2190 (ptt) REVERT: E 99 ARG cc_start: 0.7370 (mmm-85) cc_final: 0.6644 (ttt-90) REVERT: E 109 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7479 (tpp80) REVERT: E 110 ARG cc_start: 0.7299 (ttt-90) cc_final: 0.6978 (tmt170) REVERT: E 132 ARG cc_start: 0.7862 (tpt90) cc_final: 0.7512 (mmp80) REVERT: E 149 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7504 (tpt) REVERT: F 99 ARG cc_start: 0.7498 (mmm-85) cc_final: 0.6756 (ttt-90) REVERT: F 109 ARG cc_start: 0.7565 (tpp80) cc_final: 0.7362 (tpp80) REVERT: F 132 ARG cc_start: 0.7980 (tpt90) cc_final: 0.7565 (mmp80) REVERT: G 109 ARG cc_start: 0.7288 (tpp80) cc_final: 0.7048 (ttm-80) REVERT: I 148 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.8310 (m-10) outliers start: 115 outliers final: 92 residues processed: 522 average time/residue: 0.4514 time to fit residues: 369.5816 Evaluate side-chains 527 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 425 time to evaluate : 3.504 ------------------------------------------------------------------------------- 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 48 VAL Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 81 SER 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 305 LYS Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain J residue 48 VAL 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 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 66 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain M residue 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 212 THR Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 40 ILE Chi-restraints excluded: chain N residue 47 ASN Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 48 VAL 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 159 ASN 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 212 THR 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 58 ASN 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 216 ARG 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 A residue 82 LEU 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 111 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 67 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 402 optimal weight: 2.9990 chunk 360 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 327 optimal weight: 5.9990 chunk 356 optimal weight: 2.9990 chunk 56 optimal weight: 30.0000 chunk 259 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 385 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 229 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN M 30 GLN M 176 ASN P 30 GLN D 121 GLN E 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.208839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114688 restraints weight = 48066.501| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.75 r_work: 0.3018 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 31860 Z= 0.234 Angle : 0.615 9.964 42867 Z= 0.326 Chirality : 0.038 0.159 4635 Planarity : 0.004 0.060 5985 Dihedral : 3.770 45.305 4581 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.21 % Favored : 93.55 % Rotamer: Outliers : 3.69 % Allowed : 28.52 % Favored : 67.78 % 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: 2.84 (0.10), residues: 2979 sheet: -3.14 (0.52), residues: 90 loop : -3.37 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 77 HIS 0.002 0.001 HIS K 198 PHE 0.033 0.001 PHE E 112 TYR 0.008 0.001 TYR O 179 ARG 0.014 0.000 ARG J 42 Details of bonding type rmsd hydrogen bonds : bond 0.07449 ( 2290) hydrogen bonds : angle 3.69635 ( 6843) covalent geometry : bond 0.00530 (31860) covalent geometry : angle 0.61458 (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 551 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 432 time to evaluate : 3.612 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 107 ILE cc_start: 0.8470 (pt) cc_final: 0.8161 (mt) REVERT: R 260 MET cc_start: 0.0265 (mmp) cc_final: -0.0465 (mmp) REVERT: R 305 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6890 (ptpp) REVERT: J 90 MET cc_start: 0.9175 (ttm) cc_final: 0.8738 (ttm) REVERT: J 165 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8596 (ttmm) REVERT: J 220 ARG cc_start: 0.8182 (ttm110) cc_final: 0.7799 (ttp80) REVERT: K 36 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7621 (tt) REVERT: K 202 MET cc_start: 0.8583 (mmm) cc_final: 0.8208 (mmm) REVERT: K 214 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8310 (mt-10) REVERT: L 38 ASP cc_start: 0.8015 (p0) cc_final: 0.7428 (t70) REVERT: L 90 MET cc_start: 0.9406 (mtp) cc_final: 0.8949 (mtp) REVERT: L 221 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7975 (ttm110) REVERT: L 260 MET cc_start: 0.0527 (mmp) cc_final: -0.1918 (tmm) REVERT: N 95 ASP cc_start: 0.8850 (t70) cc_final: 0.8277 (t70) REVERT: N 101 ASP cc_start: 0.8879 (p0) cc_final: 0.8552 (p0) REVERT: N 119 LYS cc_start: 0.8818 (mtpt) cc_final: 0.8591 (ttmm) REVERT: O 36 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7232 (tt) REVERT: O 214 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7944 (mt-10) REVERT: P 101 ASP cc_start: 0.8908 (p0) cc_final: 0.8666 (p0) REVERT: P 188 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8013 (mm-40) REVERT: P 221 ARG cc_start: 0.8664 (tpp80) cc_final: 0.8308 (ttm110) REVERT: Q 42 ARG cc_start: 0.8313 (mtt90) cc_final: 0.7862 (mpt-90) REVERT: Q 101 ASP cc_start: 0.8809 (p0) cc_final: 0.8496 (p0) REVERT: Q 185 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8091 (tm-30) REVERT: Q 214 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8316 (tt0) REVERT: Q 221 ARG cc_start: 0.8372 (ttm110) cc_final: 0.7708 (ttm110) REVERT: Q 260 MET cc_start: -0.2255 (mmp) cc_final: -0.2884 (tmm) REVERT: A 3 TYR cc_start: 0.0976 (OUTLIER) cc_final: -0.0147 (p90) REVERT: A 99 ARG cc_start: 0.7655 (mmm-85) cc_final: 0.6877 (ttt-90) REVERT: A 110 ARG cc_start: 0.7821 (ttt-90) cc_final: 0.7534 (tmt170) REVERT: B 35 MET cc_start: 0.0230 (OUTLIER) cc_final: -0.0935 (tmm) REVERT: B 104 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7608 (tm-30) REVERT: B 111 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7773 (mt0) REVERT: C 1 MET cc_start: 0.4282 (pmm) cc_final: 0.3275 (ppp) REVERT: C 8 MET cc_start: 0.1105 (mmm) cc_final: 0.0705 (mtm) REVERT: C 33 MET cc_start: 0.1104 (ttp) cc_final: 0.0758 (ttp) REVERT: C 51 MET cc_start: 0.3346 (mmp) cc_final: 0.2354 (mtm) REVERT: C 111 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8315 (mp10) REVERT: D 51 MET cc_start: 0.2395 (mmm) cc_final: 0.2166 (tpt) REVERT: D 111 GLN cc_start: 0.8821 (pp30) cc_final: 0.8391 (pt0) REVERT: E 35 MET cc_start: -0.1862 (pmm) cc_final: -0.2183 (ptt) REVERT: E 99 ARG cc_start: 0.7568 (mmm-85) cc_final: 0.6872 (ttt-90) REVERT: E 109 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7618 (tpp80) REVERT: E 110 ARG cc_start: 0.7430 (ttt-90) cc_final: 0.6991 (tmt170) REVERT: E 132 ARG cc_start: 0.7892 (tpt90) cc_final: 0.7512 (mmp80) REVERT: E 149 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7527 (tpt) REVERT: E 155 ARG cc_start: 0.6176 (tmm-80) cc_final: 0.5297 (ttp80) REVERT: F 99 ARG cc_start: 0.7593 (mmm-85) cc_final: 0.6878 (ttt-90) REVERT: F 132 ARG cc_start: 0.7939 (tpt90) cc_final: 0.7537 (mmp80) REVERT: G 109 ARG cc_start: 0.7431 (tpp80) cc_final: 0.7073 (ttm-80) REVERT: H 111 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8073 (mp10) REVERT: I 148 TYR cc_start: 0.9065 (OUTLIER) cc_final: 0.8493 (m-10) outliers start: 119 outliers final: 95 residues processed: 523 average time/residue: 0.4600 time to fit residues: 372.7280 Evaluate side-chains 534 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 427 time to evaluate : 3.225 ------------------------------------------------------------------------------- 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 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 165 LYS Chi-restraints excluded: chain J residue 168 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 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 157 LEU 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 66 VAL Chi-restraints excluded: chain L residue 124 GLN 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 228 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 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 81 SER Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 48 VAL 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 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 216 ARG 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 A residue 79 LEU Chi-restraints excluded: chain A residue 82 LEU 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 111 GLN 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 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 F residue 74 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 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: 0.6980 chunk 92 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 133 optimal weight: 0.0470 chunk 77 optimal weight: 0.7980 chunk 332 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 122 optimal weight: 0.9980 chunk 233 optimal weight: 0.0370 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN J 176 ASN K 176 ASN L 176 ASN M 176 ASN N 176 ASN O 176 ASN P 176 ASN C 121 GLN D 121 GLN F 111 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.215213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121762 restraints weight = 49066.440| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.98 r_work: 0.3106 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31860 Z= 0.133 Angle : 0.559 11.806 42867 Z= 0.289 Chirality : 0.035 0.158 4635 Planarity : 0.003 0.049 5985 Dihedral : 3.533 42.315 4581 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.70 % Favored : 94.06 % Rotamer: Outliers : 2.36 % Allowed : 29.89 % Favored : 67.75 % 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: 2.32 (0.14), residues: 4122 helix: 3.11 (0.10), residues: 2961 sheet: None (None), residues: 0 loop : -3.06 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 77 HIS 0.001 0.000 HIS O 198 PHE 0.030 0.001 PHE A 112 TYR 0.012 0.001 TYR L 62 ARG 0.014 0.000 ARG J 42 Details of bonding type rmsd hydrogen bonds : bond 0.06245 ( 2290) hydrogen bonds : angle 3.36619 ( 6843) covalent geometry : bond 0.00258 (31860) covalent geometry : angle 0.55912 (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 516 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 440 time to evaluate : 4.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 95 ASP cc_start: 0.8155 (t70) cc_final: 0.7647 (t70) REVERT: R 260 MET cc_start: 0.0125 (mmp) cc_final: -0.0560 (mmp) REVERT: J 90 MET cc_start: 0.9076 (ttm) cc_final: 0.8641 (ttm) REVERT: J 185 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8169 (tm-30) REVERT: J 217 ASP cc_start: 0.8746 (t0) cc_final: 0.8307 (t0) REVERT: J 220 ARG cc_start: 0.8174 (ttm110) cc_final: 0.7864 (ttp80) REVERT: K 36 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7527 (tt) REVERT: K 90 MET cc_start: 0.8412 (mtp) cc_final: 0.8173 (mtt) REVERT: K 214 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8358 (mt-10) REVERT: L 38 ASP cc_start: 0.8061 (p0) cc_final: 0.7416 (t70) REVERT: L 90 MET cc_start: 0.9251 (mtp) cc_final: 0.8963 (mtp) REVERT: L 101 ASP cc_start: 0.8805 (p0) cc_final: 0.8484 (p0) REVERT: N 95 ASP cc_start: 0.8735 (t70) cc_final: 0.8177 (t70) REVERT: N 101 ASP cc_start: 0.8820 (p0) cc_final: 0.8537 (p0) REVERT: N 159 ASN cc_start: 0.9288 (t0) cc_final: 0.8916 (t0) REVERT: N 214 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8066 (mt-10) REVERT: O 36 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7304 (tt) REVERT: O 42 ARG cc_start: 0.7971 (ptp90) cc_final: 0.7557 (ptp90) REVERT: O 159 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8683 (t0) REVERT: O 214 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7923 (mt-10) REVERT: P 216 ARG cc_start: 0.8040 (mtp180) cc_final: 0.7777 (ttm170) REVERT: P 221 ARG cc_start: 0.8529 (tpp80) cc_final: 0.8176 (ttm110) REVERT: Q 42 ARG cc_start: 0.8145 (mtt90) cc_final: 0.7704 (mpt-90) REVERT: Q 101 ASP cc_start: 0.8780 (p0) cc_final: 0.8435 (p0) REVERT: Q 185 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8027 (tm-30) REVERT: Q 214 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8294 (tt0) REVERT: Q 221 ARG cc_start: 0.8265 (ttm110) cc_final: 0.7639 (ttm110) REVERT: Q 260 MET cc_start: -0.2345 (mmp) cc_final: -0.2943 (tmm) REVERT: A 3 TYR cc_start: 0.0936 (OUTLIER) cc_final: -0.0158 (p90) REVERT: B 35 MET cc_start: 0.0221 (OUTLIER) cc_final: -0.0911 (tmm) REVERT: B 104 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 111 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: C 1 MET cc_start: 0.4125 (pmm) cc_final: 0.3241 (ppp) REVERT: C 8 MET cc_start: 0.1085 (mmm) cc_final: 0.0694 (mtm) REVERT: C 33 MET cc_start: 0.1083 (ttp) cc_final: 0.0744 (ttp) REVERT: C 51 MET cc_start: 0.3715 (mmp) cc_final: 0.2426 (mtm) REVERT: C 111 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8250 (mp10) REVERT: D 51 MET cc_start: 0.2226 (mmm) cc_final: 0.2009 (tpt) REVERT: D 111 GLN cc_start: 0.8772 (pp30) cc_final: 0.8400 (pt0) REVERT: E 35 MET cc_start: -0.1887 (pmm) cc_final: -0.2192 (ptt) REVERT: E 99 ARG cc_start: 0.7372 (mmm-85) cc_final: 0.6634 (ttt-90) REVERT: E 109 ARG cc_start: 0.8018 (ttm-80) cc_final: 0.7470 (tpp80) REVERT: E 132 ARG cc_start: 0.7808 (tpt90) cc_final: 0.7440 (mmp80) REVERT: E 149 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7503 (tpt) REVERT: F 99 ARG cc_start: 0.7571 (mmm-85) cc_final: 0.6904 (ttt-90) REVERT: F 132 ARG cc_start: 0.8058 (tpt90) cc_final: 0.7633 (mmp80) REVERT: G 109 ARG cc_start: 0.7337 (tpp80) cc_final: 0.7044 (ttm-80) REVERT: I 148 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8317 (m-10) outliers start: 76 outliers final: 66 residues processed: 492 average time/residue: 0.5627 time to fit residues: 434.1253 Evaluate side-chains 504 residues out of total 3222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 429 time to evaluate : 5.654 ------------------------------------------------------------------------------- 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 105 LYS Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 212 THR 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 126 GLU 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 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 228 LEU 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 66 VAL Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain Q residue 216 ARG 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 82 LEU 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 111 GLN 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 19 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 114 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 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 100 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 264 optimal weight: 0.0170 chunk 232 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 chunk 306 optimal weight: 0.6980 chunk 223 optimal weight: 0.6980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN K 159 ASN D 121 GLN E 111 GLN F 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.214537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.122293 restraints weight = 48537.026| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.90 r_work: 0.3101 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31860 Z= 0.139 Angle : 0.564 13.363 42867 Z= 0.291 Chirality : 0.035 0.158 4635 Planarity : 0.003 0.047 5985 Dihedral : 3.486 41.468 4581 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.82 % Favored : 93.93 % Rotamer: Outliers : 2.64 % Allowed : 29.64 % Favored : 67.72 % 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: 2.36 (0.14), residues: 4122 helix: 3.14 (0.10), residues: 2961 sheet: None (None), residues: 0 loop : -3.04 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 77 HIS 0.000 0.000 HIS R 198 PHE 0.029 0.001 PHE E 112 TYR 0.011 0.001 TYR L 62 ARG 0.013 0.000 ARG J 42 Details of bonding type rmsd hydrogen bonds : bond 0.06297 ( 2290) hydrogen bonds : angle 3.35088 ( 6843) covalent geometry : bond 0.00285 (31860) covalent geometry : angle 0.56380 (42867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23895.70 seconds wall clock time: 414 minutes 21.13 seconds (24861.13 seconds total)