Starting phenix.real_space_refine on Thu Mar 13 19:45:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yon_33984/03_2025/7yon_33984.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yon_33984/03_2025/7yon_33984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yon_33984/03_2025/7yon_33984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yon_33984/03_2025/7yon_33984.map" model { file = "/net/cci-nas-00/data/ceres_data/7yon_33984/03_2025/7yon_33984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yon_33984/03_2025/7yon_33984.cif" } resolution = 2.95 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= 0.009 sd= 0.033 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 61 5.16 5 C 5839 2.51 5 N 1555 2.21 5 O 1706 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9161 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1764 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2581 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "L" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 223 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain breaks: 1 Chain: "R" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2402 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 10, 'TRANS': 291} Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.48, per 1000 atoms: 0.71 Number of scatterers: 9161 At special positions: 0 Unit cell: (95.937, 121.407, 140.085, 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 61 16.00 O 1706 8.00 N 1555 7.00 C 5839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 123 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.34 Conformation dependent library (CDL) restraints added in 1.1 seconds 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2186 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 38.6% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.548A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.762A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 278 removed outlier: 4.211A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.504A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.659A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.583A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'L' and resid 18 through 32 removed outlier: 3.678A pdb=" N ALA L 22 " --> pdb=" O ASN L 18 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER L 23 " --> pdb=" O ARG L 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 45 removed outlier: 3.677A pdb=" N LYS R 45 " --> pdb=" O ASP R 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 46 through 78 removed outlier: 3.908A pdb=" N VAL R 52 " --> pdb=" O GLU R 48 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE R 66 " --> pdb=" O LEU R 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL R 71 " --> pdb=" O GLY R 67 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE R 72 " --> pdb=" O ASN R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 114 removed outlier: 3.533A pdb=" N PHE R 88 " --> pdb=" O VAL R 84 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE R 89 " --> pdb=" O THR R 85 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL R 99 " --> pdb=" O ALA R 95 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN R 100 " --> pdb=" O ASP R 96 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU R 104 " --> pdb=" O ASN R 100 " (cutoff:3.500A) Proline residue: R 105 - end of helix Processing helix chain 'R' and resid 119 through 124 removed outlier: 3.758A pdb=" N HIS R 124 " --> pdb=" O PRO R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 154 removed outlier: 3.570A pdb=" N ILE R 144 " --> pdb=" O THR R 140 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA R 145 " --> pdb=" O LEU R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 180 Processing helix chain 'R' and resid 180 through 186 removed outlier: 4.206A pdb=" N ALA R 184 " --> pdb=" O ALA R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 228 removed outlier: 4.302A pdb=" N THR R 217 " --> pdb=" O SER R 213 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER R 220 " --> pdb=" O GLY R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 248 Processing helix chain 'R' and resid 255 through 294 removed outlier: 3.749A pdb=" N TYR R 259 " --> pdb=" O ALA R 255 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS R 260 " --> pdb=" O ASN R 256 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG R 262 " --> pdb=" O HIS R 258 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS R 265 " --> pdb=" O GLN R 261 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR R 266 " --> pdb=" O ARG R 262 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS R 272 " --> pdb=" O LYS R 268 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL R 273 " --> pdb=" O MET R 269 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL R 274 " --> pdb=" O LEU R 270 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.502A pdb=" N GLN R 288 " --> pdb=" O LEU R 284 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 315 Processing helix chain 'R' and resid 316 through 326 Proline residue: R 322 - end of helix Processing helix chain 'R' and resid 329 through 341 removed outlier: 3.517A pdb=" N ALA R 335 " --> pdb=" O ASN R 331 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU R 337 " --> pdb=" O ARG R 333 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG R 341 " --> pdb=" O LEU R 337 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.602A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.274A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.942A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 9.306A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.657A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.876A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.841A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.529A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.913A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.722A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.731A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 187 through 192 Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.846A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.501A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142 removed outlier: 4.055A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.552A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 removed outlier: 4.127A pdb=" N THR S 238 " --> pdb=" O GLN S 231 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1248 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: 2.74 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1479 1.31 - 1.43: 2566 1.43 - 1.56: 5215 1.56 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 9347 Sorted by residual: bond pdb=" C TYC L 36 " pdb=" NXT TYC L 36 " ideal model delta sigma weight residual 1.340 1.449 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C TYC L 36 " pdb=" O TYC L 36 " ideal model delta sigma weight residual 1.231 1.183 0.048 2.00e-02 2.50e+03 5.80e+00 bond pdb=" CZ TYC L 36 " pdb=" OH TYC L 36 " ideal model delta sigma weight residual 1.350 1.397 -0.047 2.00e-02 2.50e+03 5.57e+00 bond pdb=" C VAL S 149 " pdb=" N THR S 150 " ideal model delta sigma weight residual 1.333 1.367 -0.035 2.74e-02 1.33e+03 1.60e+00 bond pdb=" CB TYC L 36 " pdb=" CG TYC L 36 " ideal model delta sigma weight residual 1.501 1.524 -0.023 2.00e-02 2.50e+03 1.31e+00 ... (remaining 9342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 12477 1.60 - 3.21: 146 3.21 - 4.81: 30 4.81 - 6.41: 4 6.41 - 8.02: 2 Bond angle restraints: 12659 Sorted by residual: angle pdb=" N CYS B 233 " pdb=" CA CYS B 233 " pdb=" C CYS B 233 " ideal model delta sigma weight residual 108.32 112.45 -4.13 1.64e+00 3.72e-01 6.35e+00 angle pdb=" N GLU L 6 " pdb=" CA GLU L 6 " pdb=" CB GLU L 6 " ideal model delta sigma weight residual 113.65 110.19 3.46 1.47e+00 4.63e-01 5.53e+00 angle pdb=" C VAL S 149 " pdb=" N THR S 150 " pdb=" CA THR S 150 " ideal model delta sigma weight residual 122.15 130.17 -8.02 3.47e+00 8.31e-02 5.34e+00 angle pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta sigma weight residual 121.54 125.89 -4.35 1.91e+00 2.74e-01 5.19e+00 angle pdb=" CA LEU S 219 " pdb=" CB LEU S 219 " pdb=" CG LEU S 219 " ideal model delta sigma weight residual 116.30 123.26 -6.96 3.50e+00 8.16e-02 3.95e+00 ... (remaining 12654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 5013 17.51 - 35.03: 442 35.03 - 52.54: 85 52.54 - 70.05: 18 70.05 - 87.56: 5 Dihedral angle restraints: 5563 sinusoidal: 2175 harmonic: 3388 Sorted by residual: dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual 93.00 149.94 -56.94 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CG ARG B 22 " pdb=" CD ARG B 22 " pdb=" NE ARG B 22 " pdb=" CZ ARG B 22 " ideal model delta sinusoidal sigma weight residual 180.00 135.31 44.69 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU A 298 " pdb=" CG GLU A 298 " pdb=" CD GLU A 298 " pdb=" OE1 GLU A 298 " ideal model delta sinusoidal sigma weight residual 0.00 86.42 -86.42 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 5560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 883 0.031 - 0.061: 394 0.061 - 0.092: 98 0.092 - 0.123: 64 0.123 - 0.154: 7 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CA ILE R 195 " pdb=" N ILE R 195 " pdb=" C ILE R 195 " pdb=" CB ILE R 195 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA ILE S 189 " pdb=" N ILE S 189 " pdb=" C ILE S 189 " pdb=" CB ILE S 189 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE S 157 " pdb=" N ILE S 157 " pdb=" C ILE S 157 " pdb=" CB ILE S 157 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 1443 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 195 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.35e+00 pdb=" N PRO R 196 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO R 196 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 196 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER S 184 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO S 185 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO S 185 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO S 185 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 110 " 0.011 2.00e-02 2.50e+03 8.79e-03 1.55e+00 pdb=" CG TYR R 110 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR R 110 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR R 110 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR R 110 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 110 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR R 110 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 110 " 0.001 2.00e-02 2.50e+03 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 179 2.70 - 3.25: 8380 3.25 - 3.80: 13196 3.80 - 4.35: 17751 4.35 - 4.90: 31270 Nonbonded interactions: 70776 Sorted by model distance: nonbonded pdb=" O ASP B 333 " pdb=" OD1 ASP B 333 " model vdw 2.155 3.040 nonbonded pdb=" OD1 ASP B 153 " pdb=" N ASP B 154 " model vdw 2.195 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.196 3.040 nonbonded pdb=" NE2 GLN S 179 " pdb=" O GLN S 183 " model vdw 2.320 3.120 nonbonded pdb=" OE1 GLN L 34 " pdb=" O HOH L 101 " model vdw 2.323 3.040 ... (remaining 70771 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.160 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: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.570 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 : 0.003 0.109 9347 Z= 0.214 Angle : 0.488 8.017 12659 Z= 0.249 Chirality : 0.041 0.154 1446 Planarity : 0.003 0.052 1591 Dihedral : 13.736 87.563 3368 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 0.20 (0.24), residues: 1145 helix: 0.14 (0.24), residues: 394 sheet: 1.23 (0.31), residues: 282 loop : -0.46 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE A 354 TYR 0.021 0.001 TYR R 110 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.987 Fit side-chains REVERT: A 21 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7510 (mtm110) REVERT: A 209 LYS cc_start: 0.9020 (ttpp) cc_final: 0.8792 (tttp) REVERT: B 134 ARG cc_start: 0.7950 (ptt90) cc_final: 0.7720 (ptt-90) REVERT: R 96 ASP cc_start: 0.7546 (m-30) cc_final: 0.7313 (m-30) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 1.4986 time to fit residues: 246.6287 Evaluate side-chains 137 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.2980 chunk 86 optimal weight: 0.4980 chunk 47 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 230 ASN B 340 ASN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.126493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.100834 restraints weight = 14303.825| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.71 r_work: 0.3077 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9347 Z= 0.183 Angle : 0.538 6.934 12659 Z= 0.288 Chirality : 0.042 0.155 1446 Planarity : 0.004 0.053 1591 Dihedral : 4.559 46.027 1269 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.40 % Allowed : 8.67 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.23 (0.25), residues: 1145 helix: 1.97 (0.26), residues: 380 sheet: 1.24 (0.30), residues: 293 loop : -0.41 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.005 0.001 HIS R 73 PHE 0.012 0.001 PHE A 189 TYR 0.017 0.001 TYR R 110 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8390 (ttm110) cc_final: 0.8062 (mtm110) REVERT: A 209 LYS cc_start: 0.9119 (ttpp) cc_final: 0.8912 (tttp) REVERT: A 306 GLN cc_start: 0.7446 (mm110) cc_final: 0.7203 (mm110) REVERT: B 20 ASP cc_start: 0.7526 (m-30) cc_final: 0.7217 (m-30) REVERT: B 23 LYS cc_start: 0.8054 (tptt) cc_final: 0.7815 (tptm) REVERT: B 170 ASP cc_start: 0.8321 (t70) cc_final: 0.8115 (t0) outliers start: 14 outliers final: 7 residues processed: 146 average time/residue: 1.3335 time to fit residues: 207.1929 Evaluate side-chains 142 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 330 SER Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 110 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 103 optimal weight: 0.0970 chunk 94 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 331 ASN R 100 ASN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.125892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.096335 restraints weight = 14437.921| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.61 r_work: 0.3061 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9347 Z= 0.202 Angle : 0.524 6.884 12659 Z= 0.277 Chirality : 0.042 0.154 1446 Planarity : 0.003 0.053 1591 Dihedral : 4.415 40.029 1269 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.30 % Allowed : 11.47 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.42 (0.25), residues: 1145 helix: 2.36 (0.27), residues: 382 sheet: 1.24 (0.30), residues: 286 loop : -0.43 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.021 0.001 TYR R 110 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8375 (ttm110) cc_final: 0.7983 (mtm110) REVERT: B 20 ASP cc_start: 0.7485 (m-30) cc_final: 0.7208 (m-30) REVERT: B 23 LYS cc_start: 0.7992 (tptt) cc_final: 0.7757 (tptm) REVERT: B 170 ASP cc_start: 0.8343 (t70) cc_final: 0.8081 (t0) REVERT: G 42 GLU cc_start: 0.7674 (mp0) cc_final: 0.7407 (mp0) outliers start: 13 outliers final: 10 residues processed: 139 average time/residue: 1.3776 time to fit residues: 203.0215 Evaluate side-chains 136 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 222 SER Chi-restraints excluded: chain R residue 330 SER Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 80 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 105 optimal weight: 0.0370 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS R 100 ASN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.126577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.097103 restraints weight = 14321.614| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.61 r_work: 0.3071 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9347 Z= 0.167 Angle : 0.495 7.339 12659 Z= 0.262 Chirality : 0.041 0.154 1446 Planarity : 0.003 0.054 1591 Dihedral : 4.051 27.679 1269 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.49 % Allowed : 12.96 % Favored : 84.55 % 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: 1.52 (0.25), residues: 1145 helix: 2.39 (0.27), residues: 389 sheet: 1.27 (0.30), residues: 290 loop : -0.36 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.015 0.001 TYR S 190 ARG 0.006 0.000 ARG R 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8184 (ttm110) cc_final: 0.7781 (mtm110) REVERT: B 20 ASP cc_start: 0.7388 (m-30) cc_final: 0.7157 (m-30) REVERT: B 23 LYS cc_start: 0.7978 (tptt) cc_final: 0.7743 (tptm) REVERT: B 170 ASP cc_start: 0.8107 (t70) cc_final: 0.7899 (t0) REVERT: B 195 ASP cc_start: 0.6789 (OUTLIER) cc_final: 0.6529 (p0) REVERT: L 24 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7329 (mm) REVERT: S 87 ARG cc_start: 0.8500 (ptp-170) cc_final: 0.8210 (mtp180) outliers start: 25 outliers final: 12 residues processed: 145 average time/residue: 1.3274 time to fit residues: 204.7037 Evaluate side-chains 140 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 222 SER Chi-restraints excluded: chain R residue 226 ILE Chi-restraints excluded: chain R residue 330 SER Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 116 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS R 100 ASN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.125570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096039 restraints weight = 14268.530| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.57 r_work: 0.3043 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9347 Z= 0.222 Angle : 0.540 7.558 12659 Z= 0.282 Chirality : 0.043 0.153 1446 Planarity : 0.003 0.054 1591 Dihedral : 4.026 19.897 1269 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.89 % Allowed : 13.66 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.40 (0.25), residues: 1145 helix: 2.34 (0.27), residues: 389 sheet: 1.20 (0.30), residues: 281 loop : -0.44 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE A 189 TYR 0.021 0.001 TYR R 110 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8162 (ttm110) cc_final: 0.7772 (mtm110) REVERT: B 20 ASP cc_start: 0.7429 (m-30) cc_final: 0.7143 (m-30) REVERT: B 23 LYS cc_start: 0.8033 (tptt) cc_final: 0.7807 (tptm) REVERT: B 195 ASP cc_start: 0.6668 (OUTLIER) cc_final: 0.6467 (p0) REVERT: G 42 GLU cc_start: 0.7547 (mp0) cc_final: 0.7329 (mp0) REVERT: L 24 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7357 (mm) REVERT: S 202 ARG cc_start: 0.7900 (ptp90) cc_final: 0.7658 (ptp90) outliers start: 29 outliers final: 14 residues processed: 148 average time/residue: 1.3915 time to fit residues: 220.1486 Evaluate side-chains 143 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 222 SER Chi-restraints excluded: chain R residue 330 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS R 100 ASN R 261 GLN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.125469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.099807 restraints weight = 14183.749| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.70 r_work: 0.3059 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9347 Z= 0.223 Angle : 0.542 7.951 12659 Z= 0.284 Chirality : 0.043 0.152 1446 Planarity : 0.003 0.055 1591 Dihedral : 4.009 21.333 1269 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.59 % Allowed : 14.66 % Favored : 82.75 % 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: 1.39 (0.25), residues: 1145 helix: 2.34 (0.27), residues: 388 sheet: 1.15 (0.30), residues: 282 loop : -0.43 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.019 0.001 TYR R 110 ARG 0.006 0.000 ARG R 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8360 (ttm110) cc_final: 0.7943 (mtm110) REVERT: B 23 LYS cc_start: 0.8021 (tptt) cc_final: 0.7787 (tptm) REVERT: B 195 ASP cc_start: 0.6592 (OUTLIER) cc_final: 0.6368 (p0) REVERT: L 24 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7496 (mm) REVERT: S 89 GLU cc_start: 0.7570 (mp0) cc_final: 0.7276 (pm20) outliers start: 26 outliers final: 15 residues processed: 143 average time/residue: 1.3011 time to fit residues: 198.0757 Evaluate side-chains 143 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 222 SER Chi-restraints excluded: chain R residue 330 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS R 100 ASN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.125402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.096055 restraints weight = 14394.974| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.56 r_work: 0.3055 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9347 Z= 0.214 Angle : 0.536 8.478 12659 Z= 0.281 Chirality : 0.043 0.153 1446 Planarity : 0.003 0.055 1591 Dihedral : 3.983 22.211 1269 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.29 % Allowed : 15.65 % Favored : 82.05 % 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: 1.38 (0.25), residues: 1145 helix: 2.31 (0.28), residues: 389 sheet: 1.16 (0.30), residues: 281 loop : -0.42 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.018 0.001 TYR R 110 ARG 0.007 0.000 ARG R 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 2.438 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7867 (mtm110) REVERT: B 23 LYS cc_start: 0.7989 (tptt) cc_final: 0.7755 (tptm) REVERT: B 195 ASP cc_start: 0.6440 (OUTLIER) cc_final: 0.6226 (p0) REVERT: L 24 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7493 (mm) REVERT: R 98 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7474 (mm) outliers start: 23 outliers final: 14 residues processed: 137 average time/residue: 1.4687 time to fit residues: 214.8392 Evaluate side-chains 141 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 222 SER Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 95 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 101 optimal weight: 0.1980 chunk 3 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS R 100 ASN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.125900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.096113 restraints weight = 14566.210| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.62 r_work: 0.3064 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9347 Z= 0.214 Angle : 0.535 8.747 12659 Z= 0.280 Chirality : 0.043 0.152 1446 Planarity : 0.003 0.055 1591 Dihedral : 3.985 22.807 1269 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.69 % Allowed : 15.75 % Favored : 81.56 % 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: 1.35 (0.25), residues: 1145 helix: 2.30 (0.27), residues: 389 sheet: 1.14 (0.30), residues: 280 loop : -0.44 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.017 0.001 TYR R 110 ARG 0.007 0.000 ARG R 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.954 Fit side-chains revert: symmetry clash REVERT: A 4 THR cc_start: 0.6835 (OUTLIER) cc_final: 0.6579 (t) REVERT: A 21 ARG cc_start: 0.8083 (ttm110) cc_final: 0.7660 (mtm110) REVERT: B 23 LYS cc_start: 0.7944 (tptt) cc_final: 0.7716 (tptm) REVERT: B 46 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7851 (mpt-90) REVERT: L 24 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7309 (mm) REVERT: R 98 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7470 (mm) REVERT: R 261 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6651 (mp10) REVERT: S 89 GLU cc_start: 0.7394 (mp0) cc_final: 0.7074 (pm20) outliers start: 27 outliers final: 16 residues processed: 144 average time/residue: 1.4247 time to fit residues: 219.9043 Evaluate side-chains 145 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 222 SER Chi-restraints excluded: chain R residue 261 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 100 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 0.2980 chunk 69 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 92 optimal weight: 0.2980 chunk 110 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS R 100 ASN S 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.126807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.096988 restraints weight = 14297.097| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.64 r_work: 0.3082 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9347 Z= 0.171 Angle : 0.510 8.944 12659 Z= 0.268 Chirality : 0.042 0.152 1446 Planarity : 0.003 0.055 1591 Dihedral : 3.890 21.838 1269 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.49 % Allowed : 16.25 % Favored : 81.26 % 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: 1.43 (0.25), residues: 1145 helix: 2.37 (0.28), residues: 390 sheet: 1.21 (0.30), residues: 285 loop : -0.45 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.015 0.001 TYR S 235 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.987 Fit side-chains revert: symmetry clash REVERT: A 4 THR cc_start: 0.7013 (OUTLIER) cc_final: 0.6698 (t) REVERT: A 21 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7865 (mtm110) REVERT: B 23 LYS cc_start: 0.7987 (tptt) cc_final: 0.7755 (tptm) REVERT: B 44 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7678 (mt0) REVERT: B 46 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.8135 (mpt-90) REVERT: G 42 GLU cc_start: 0.7557 (mp0) cc_final: 0.7251 (mp0) REVERT: L 24 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7481 (mm) REVERT: R 98 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7454 (mm) REVERT: R 261 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6803 (mp10) outliers start: 25 outliers final: 18 residues processed: 141 average time/residue: 1.3173 time to fit residues: 197.5805 Evaluate side-chains 148 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 222 SER Chi-restraints excluded: chain R residue 261 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 112 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS R 68 ASN R 100 ASN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.126087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.096289 restraints weight = 14492.950| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.63 r_work: 0.3044 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9347 Z= 0.236 Angle : 0.560 9.075 12659 Z= 0.293 Chirality : 0.043 0.152 1446 Planarity : 0.004 0.055 1591 Dihedral : 4.003 23.052 1269 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.79 % Allowed : 16.25 % Favored : 80.96 % 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: 1.30 (0.25), residues: 1145 helix: 2.28 (0.27), residues: 389 sheet: 1.14 (0.30), residues: 280 loop : -0.52 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.012 0.001 PHE B 199 TYR 0.019 0.002 TYR R 110 ARG 0.007 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8107 (ttm110) cc_final: 0.7807 (mtm110) REVERT: B 23 LYS cc_start: 0.8003 (tptt) cc_final: 0.7776 (tptm) REVERT: B 44 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7578 (mt0) REVERT: B 46 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7919 (mpt-90) REVERT: B 129 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6777 (tmt170) REVERT: L 24 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7379 (mm) REVERT: R 98 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7439 (mm) REVERT: R 261 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6675 (mp10) outliers start: 28 outliers final: 18 residues processed: 139 average time/residue: 1.3899 time to fit residues: 206.4250 Evaluate side-chains 148 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 129 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain R residue 68 ASN Chi-restraints excluded: chain R residue 98 LEU Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 151 CYS Chi-restraints excluded: chain R residue 222 SER Chi-restraints excluded: chain R residue 261 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 6 optimal weight: 0.0170 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 195 HIS R 68 ASN R 100 ASN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.126114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.096227 restraints weight = 14344.886| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.63 r_work: 0.3054 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 9347 Z= 0.279 Angle : 0.886 59.199 12659 Z= 0.523 Chirality : 0.049 0.913 1446 Planarity : 0.004 0.055 1591 Dihedral : 4.139 39.807 1269 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.10 % Favored : 97.82 % Rotamer: Outliers : 2.59 % Allowed : 16.35 % Favored : 81.06 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.29 (0.25), residues: 1145 helix: 2.26 (0.28), residues: 389 sheet: 1.14 (0.30), residues: 280 loop : -0.52 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE B 199 TYR 0.018 0.001 TYR R 110 ARG 0.006 0.000 ARG R 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7838.93 seconds wall clock time: 137 minutes 23.10 seconds (8243.10 seconds total)