Starting phenix.real_space_refine on Wed Aug 5 21:24:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21fj_67627/08_2026/21fj_67627.cif Found real_map, /net/cci-nas-00/data/ceres_data/21fj_67627/08_2026/21fj_67627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21fj_67627/08_2026/21fj_67627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21fj_67627/08_2026/21fj_67627.map" model { file = "/net/cci-nas-00/data/ceres_data/21fj_67627/08_2026/21fj_67627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21fj_67627/08_2026/21fj_67627.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.087 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 63 5.16 5 C 7782 2.51 5 N 1755 2.21 5 O 1989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11589 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3863 Classifications: {'peptide': 500} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 20, 'TRANS': 479} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C Time building chain proxies: 2.91, per 1000 atoms: 0.25 Number of scatterers: 11589 At special positions: 0 Unit cell: (117.693, 116.4, 80.1865, 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 63 16.00 O 1989 8.00 N 1755 7.00 C 7782 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: 0.99 Conformation dependent library (CDL) restraints added in 517.0 milliseconds 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 8 through 28 removed outlier: 3.693A pdb=" N THR A 14 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) Proline residue: A 24 - end of helix Processing helix chain 'A' and resid 28 through 47 Processing helix chain 'A' and resid 48 through 67 removed outlier: 3.831A pdb=" N LEU A 52 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.570A pdb=" N ILE A 73 " --> pdb=" O HIS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 97 through 109 removed outlier: 4.213A pdb=" N GLY A 101 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 114 removed outlier: 3.813A pdb=" N TYR A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 140 removed outlier: 4.292A pdb=" N ALA A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.773A pdb=" N TRP A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 161 removed outlier: 3.997A pdb=" N ILE A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.771A pdb=" N LEU A 198 " --> pdb=" O MET A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 220 removed outlier: 3.952A pdb=" N THR A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Proline residue: A 210 - end of helix removed outlier: 3.520A pdb=" N ALA A 213 " --> pdb=" O THR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 247 removed outlier: 3.856A pdb=" N THR A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TRP A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 274 removed outlier: 3.777A pdb=" N ILE A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 293 removed outlier: 3.776A pdb=" N THR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 313 through 324 removed outlier: 3.508A pdb=" N TYR A 324 " --> pdb=" O TRP A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.657A pdb=" N LEU A 330 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 373 removed outlier: 3.901A pdb=" N TRP A 351 " --> pdb=" O GLY A 347 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS A 356 " --> pdb=" O GLY A 352 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.810A pdb=" N GLU A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.992A pdb=" N MET A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 431 removed outlier: 3.562A pdb=" N THR A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 451 Processing helix chain 'A' and resid 454 through 464 removed outlier: 3.582A pdb=" N GLY A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 478 removed outlier: 3.576A pdb=" N LEU A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA A 473 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 499 removed outlier: 4.008A pdb=" N GLY A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.693A pdb=" N THR B 14 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) Proline residue: B 24 - end of helix Processing helix chain 'B' and resid 28 through 47 Processing helix chain 'B' and resid 48 through 67 removed outlier: 3.831A pdb=" N LEU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 73 removed outlier: 3.571A pdb=" N ILE B 73 " --> pdb=" O HIS B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 96 Processing helix chain 'B' and resid 97 through 109 removed outlier: 4.213A pdb=" N GLY B 101 " --> pdb=" O GLY B 97 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 102 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 103 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR B 107 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 removed outlier: 3.813A pdb=" N TYR B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 140 removed outlier: 4.292A pdb=" N ALA B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 150 removed outlier: 3.773A pdb=" N TRP B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 161 removed outlier: 3.997A pdb=" N ILE B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 194 through 199 removed outlier: 3.771A pdb=" N LEU B 198 " --> pdb=" O MET B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 220 removed outlier: 3.952A pdb=" N THR B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Proline residue: B 210 - end of helix removed outlier: 3.520A pdb=" N ALA B 213 " --> pdb=" O THR B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 247 removed outlier: 3.856A pdb=" N THR B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TRP B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 274 removed outlier: 3.777A pdb=" N ILE B 260 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N CYS B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 271 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 293 removed outlier: 3.776A pdb=" N THR B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 299 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.508A pdb=" N TYR B 324 " --> pdb=" O TRP B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.657A pdb=" N LEU B 330 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 373 removed outlier: 3.901A pdb=" N TRP B 351 " --> pdb=" O GLY B 347 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY B 355 " --> pdb=" O TRP B 351 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 383 removed outlier: 3.810A pdb=" N GLU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 396 removed outlier: 3.992A pdb=" N MET B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 431 removed outlier: 3.562A pdb=" N THR B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 Processing helix chain 'B' and resid 454 through 464 removed outlier: 3.582A pdb=" N GLY B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 478 removed outlier: 3.576A pdb=" N LEU B 470 " --> pdb=" O ASP B 466 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 499 removed outlier: 4.008A pdb=" N GLY B 499 " --> pdb=" O MET B 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 28 removed outlier: 3.693A pdb=" N THR C 14 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE C 15 " --> pdb=" O PHE C 11 " (cutoff:3.500A) Proline residue: C 24 - end of helix Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 48 through 67 removed outlier: 3.831A pdb=" N LEU C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA C 54 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.570A pdb=" N ILE C 73 " --> pdb=" O HIS C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 96 Processing helix chain 'C' and resid 97 through 109 removed outlier: 4.213A pdb=" N GLY C 101 " --> pdb=" O GLY C 97 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N TYR C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR C 107 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE C 108 " --> pdb=" O TYR C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 114 removed outlier: 3.813A pdb=" N TYR C 113 " --> pdb=" O GLU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 140 removed outlier: 4.292A pdb=" N ALA C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE C 138 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 150 removed outlier: 3.773A pdb=" N TRP C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N PHE C 147 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N PHE C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 150 " --> pdb=" O ALA C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 161 removed outlier: 3.997A pdb=" N ILE C 155 " --> pdb=" O PRO C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 194 through 199 removed outlier: 3.771A pdb=" N LEU C 198 " --> pdb=" O MET C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 220 removed outlier: 3.952A pdb=" N THR C 209 " --> pdb=" O LEU C 205 " (cutoff:3.500A) Proline residue: C 210 - end of helix removed outlier: 3.520A pdb=" N ALA C 213 " --> pdb=" O THR C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 247 removed outlier: 3.856A pdb=" N THR C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TRP C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 274 removed outlier: 3.777A pdb=" N ILE C 260 " --> pdb=" O SER C 256 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N CYS C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR C 269 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 293 removed outlier: 3.777A pdb=" N THR C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL C 287 " --> pdb=" O GLY C 283 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY C 288 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 308 through 313 Processing helix chain 'C' and resid 313 through 324 removed outlier: 3.508A pdb=" N TYR C 324 " --> pdb=" O TRP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.657A pdb=" N LEU C 330 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 373 removed outlier: 3.901A pdb=" N TRP C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY C 355 " --> pdb=" O TRP C 351 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 383 removed outlier: 3.810A pdb=" N GLU C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 396 removed outlier: 3.992A pdb=" N MET C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 431 removed outlier: 3.562A pdb=" N THR C 419 " --> pdb=" O PHE C 415 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR C 425 " --> pdb=" O ASP C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 451 Processing helix chain 'C' and resid 454 through 464 removed outlier: 3.582A pdb=" N GLY C 458 " --> pdb=" O PHE C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 478 removed outlier: 3.576A pdb=" N LEU C 470 " --> pdb=" O ASP C 466 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA C 473 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 499 removed outlier: 4.008A pdb=" N GLY C 499 " --> pdb=" O MET C 495 " (cutoff:3.500A) 681 hydrogen bonds defined for protein. 2007 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: 1.59 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1713 1.29 - 1.42: 3311 1.42 - 1.55: 6790 1.55 - 1.68: 6 1.68 - 1.81: 108 Bond restraints: 11928 Sorted by residual: bond pdb=" CA ALA C 423 " pdb=" C ALA C 423 " ideal model delta sigma weight residual 1.524 1.430 0.094 1.27e-02 6.20e+03 5.44e+01 bond pdb=" CA ALA B 423 " pdb=" C ALA B 423 " ideal model delta sigma weight residual 1.524 1.430 0.093 1.27e-02 6.20e+03 5.41e+01 bond pdb=" CA ALA A 423 " pdb=" C ALA A 423 " ideal model delta sigma weight residual 1.524 1.431 0.093 1.27e-02 6.20e+03 5.37e+01 bond pdb=" C ALA A 423 " pdb=" O ALA A 423 " ideal model delta sigma weight residual 1.236 1.164 0.073 1.15e-02 7.56e+03 4.02e+01 bond pdb=" C ALA C 423 " pdb=" O ALA C 423 " ideal model delta sigma weight residual 1.236 1.164 0.073 1.15e-02 7.56e+03 4.00e+01 ... (remaining 11923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 15780 1.81 - 3.61: 378 3.61 - 5.42: 84 5.42 - 7.23: 21 7.23 - 9.04: 3 Bond angle restraints: 16266 Sorted by residual: angle pdb=" N LEU A 453 " pdb=" CA LEU A 453 " pdb=" C LEU A 453 " ideal model delta sigma weight residual 112.92 106.01 6.91 1.23e+00 6.61e-01 3.16e+01 angle pdb=" N LEU C 453 " pdb=" CA LEU C 453 " pdb=" C LEU C 453 " ideal model delta sigma weight residual 112.92 106.01 6.91 1.23e+00 6.61e-01 3.15e+01 angle pdb=" N LEU B 453 " pdb=" CA LEU B 453 " pdb=" C LEU B 453 " ideal model delta sigma weight residual 112.92 106.02 6.90 1.23e+00 6.61e-01 3.15e+01 angle pdb=" C PHE A 454 " pdb=" CA PHE A 454 " pdb=" CB PHE A 454 " ideal model delta sigma weight residual 110.09 101.05 9.04 1.67e+00 3.59e-01 2.93e+01 angle pdb=" C PHE C 454 " pdb=" CA PHE C 454 " pdb=" CB PHE C 454 " ideal model delta sigma weight residual 110.09 101.07 9.02 1.67e+00 3.59e-01 2.92e+01 ... (remaining 16261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.69: 5692 14.69 - 29.37: 653 29.37 - 44.06: 285 44.06 - 58.75: 84 58.75 - 73.43: 15 Dihedral angle restraints: 6729 sinusoidal: 2472 harmonic: 4257 Sorted by residual: dihedral pdb=" C SER A 422 " pdb=" N SER A 422 " pdb=" CA SER A 422 " pdb=" CB SER A 422 " ideal model delta harmonic sigma weight residual -122.60 -133.08 10.48 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" C SER B 422 " pdb=" N SER B 422 " pdb=" CA SER B 422 " pdb=" CB SER B 422 " ideal model delta harmonic sigma weight residual -122.60 -133.08 10.48 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" C SER C 422 " pdb=" N SER C 422 " pdb=" CA SER C 422 " pdb=" CB SER C 422 " ideal model delta harmonic sigma weight residual -122.60 -133.05 10.45 0 2.50e+00 1.60e-01 1.75e+01 ... (remaining 6726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1795 0.085 - 0.170: 80 0.170 - 0.255: 18 0.255 - 0.341: 6 0.341 - 0.426: 6 Chirality restraints: 1905 Sorted by residual: chirality pdb=" CA ASP B 421 " pdb=" N ASP B 421 " pdb=" C ASP B 421 " pdb=" CB ASP B 421 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" CA ASP C 421 " pdb=" N ASP C 421 " pdb=" C ASP C 421 " pdb=" CB ASP C 421 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" CA ASP A 421 " pdb=" N ASP A 421 " pdb=" C ASP A 421 " pdb=" CB ASP A 421 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.53e+00 ... (remaining 1902 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 421 " 0.016 2.00e-02 2.50e+03 3.07e-02 9.42e+00 pdb=" C ASP A 421 " -0.053 2.00e-02 2.50e+03 pdb=" O ASP A 421 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 422 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 421 " -0.016 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C ASP C 421 " 0.053 2.00e-02 2.50e+03 pdb=" O ASP C 421 " -0.019 2.00e-02 2.50e+03 pdb=" N SER C 422 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 421 " 0.016 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C ASP B 421 " -0.053 2.00e-02 2.50e+03 pdb=" O ASP B 421 " 0.019 2.00e-02 2.50e+03 pdb=" N SER B 422 " 0.018 2.00e-02 2.50e+03 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 24 2.53 - 3.12: 8462 3.12 - 3.71: 17011 3.71 - 4.31: 23670 4.31 - 4.90: 40776 Nonbonded interactions: 89943 Sorted by model distance: nonbonded pdb=" O SER A 45 " pdb=" OE2 GLU C 277 " model vdw 1.937 3.040 nonbonded pdb=" OE2 GLU B 277 " pdb=" O SER C 45 " model vdw 1.937 3.040 nonbonded pdb=" OE2 GLU A 277 " pdb=" O SER B 45 " model vdw 1.938 3.040 nonbonded pdb=" O LEU B 205 " pdb=" OG1 THR B 209 " model vdw 2.216 3.040 nonbonded pdb=" O LEU A 205 " pdb=" OG1 THR A 209 " model vdw 2.216 3.040 ... (remaining 89938 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' } 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: 0.440 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.580 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 : 0.005 0.094 11928 Z= 0.363 Angle : 0.708 9.037 16266 Z= 0.449 Chirality : 0.051 0.426 1905 Planarity : 0.005 0.039 1944 Dihedral : 16.162 73.434 4023 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.41 % Allowed : 25.12 % Favored : 71.46 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.22), residues: 1494 helix: 0.14 (0.16), residues: 1152 sheet: None (None), residues: 0 loop : -1.58 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 342 TYR 0.020 0.002 TYR B 425 PHE 0.031 0.001 PHE A 454 TRP 0.013 0.001 TRP C 140 HIS 0.002 0.001 HIS C 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.36 (11928) covalent geometry : angle 0.70758 / 0.45 (16266) hydrogen bonds : bond 0.14329 / 9.42 ( 681) hydrogen bonds : angle 4.89205 / 3.44 ( 2007) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 426 MET cc_start: 0.6116 (mpp) cc_final: 0.5502 (mmm) REVERT: A 433 PRO cc_start: 0.8298 (Cg_endo) cc_final: 0.8076 (Cg_exo) REVERT: B 194 MET cc_start: 0.7956 (ttm) cc_final: 0.7301 (mmm) REVERT: B 222 ILE cc_start: 0.7158 (mp) cc_final: 0.6843 (tp) REVERT: B 377 SER cc_start: 0.7899 (OUTLIER) cc_final: 0.7039 (p) REVERT: B 392 MET cc_start: 0.7987 (mmt) cc_final: 0.7758 (mmt) REVERT: C 317 TYR cc_start: 0.8141 (m-80) cc_final: 0.7911 (m-80) outliers start: 42 outliers final: 32 residues processed: 160 average time/residue: 0.0548 time to fit residues: 14.7100 Evaluate side-chains 151 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 432 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN B 40 ASN B 298 ASN C 40 ASN C 298 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.158716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.142870 restraints weight = 11999.067| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 0.79 r_work: 0.3340 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11928 Z= 0.124 Angle : 0.481 5.478 16266 Z= 0.259 Chirality : 0.038 0.147 1905 Planarity : 0.004 0.038 1944 Dihedral : 6.103 52.496 1620 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.82 % Allowed : 22.36 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.22), residues: 1494 helix: 0.47 (0.16), residues: 1167 sheet: None (None), residues: 0 loop : -1.28 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 296 TYR 0.012 0.001 TYR B 269 PHE 0.016 0.001 PHE B 240 TRP 0.008 0.001 TRP C 321 HIS 0.002 0.001 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (11928) covalent geometry : angle 0.48082 / 0.26 (16266) hydrogen bonds : bond 0.04660 / 3.05 ( 681) hydrogen bonds : angle 3.91999 / 2.76 ( 2007) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 121 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 383 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: A 426 MET cc_start: 0.6818 (mpp) cc_final: 0.6503 (mmp) REVERT: B 194 MET cc_start: 0.8107 (ttm) cc_final: 0.7385 (mmm) REVERT: B 383 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: B 493 MET cc_start: 0.7912 (mmm) cc_final: 0.7686 (mmp) REVERT: C 228 MET cc_start: 0.6586 (mmm) cc_final: 0.6159 (ttm) REVERT: C 383 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: C 486 MET cc_start: 0.8115 (mtm) cc_final: 0.7914 (mtm) outliers start: 47 outliers final: 23 residues processed: 158 average time/residue: 0.0621 time to fit residues: 16.1570 Evaluate side-chains 145 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 318 TRP Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 318 TRP Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 21 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.154022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.138208 restraints weight = 12147.720| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 0.81 r_work: 0.3084 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 11928 Z= 0.215 Angle : 0.593 5.593 16266 Z= 0.320 Chirality : 0.041 0.159 1905 Planarity : 0.005 0.039 1944 Dihedral : 5.656 59.078 1584 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.96 % Allowed : 22.93 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.21), residues: 1494 helix: 0.12 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -1.53 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 296 TYR 0.018 0.002 TYR A 269 PHE 0.020 0.002 PHE B 240 TRP 0.014 0.002 TRP C 313 HIS 0.005 0.001 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.21 (11928) covalent geometry : angle 0.59275 / 0.32 (16266) hydrogen bonds : bond 0.06599 / 4.30 ( 681) hydrogen bonds : angle 4.27953 / 3.00 ( 2007) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 117 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.6160 (mmp) REVERT: B 194 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7457 (mmm) REVERT: B 383 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8119 (mp0) REVERT: C 246 SER cc_start: 0.7864 (OUTLIER) cc_final: 0.7258 (t) REVERT: C 359 TYR cc_start: 0.8239 (OUTLIER) cc_final: 0.7939 (m-80) outliers start: 61 outliers final: 44 residues processed: 159 average time/residue: 0.0625 time to fit residues: 16.2544 Evaluate side-chains 166 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 117 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 318 TRP Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 318 TRP Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 112 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.158501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.142509 restraints weight = 12077.123| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 0.79 r_work: 0.3221 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work: 0.3050 rms_B_bonded: 4.31 restraints_weight: 0.1250 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11928 Z= 0.123 Angle : 0.473 5.352 16266 Z= 0.255 Chirality : 0.037 0.147 1905 Planarity : 0.004 0.036 1944 Dihedral : 5.325 58.294 1584 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.47 % Allowed : 24.15 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.22), residues: 1494 helix: 0.38 (0.16), residues: 1158 sheet: None (None), residues: 0 loop : -1.27 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 296 TYR 0.012 0.001 TYR A 269 PHE 0.014 0.001 PHE B 240 TRP 0.008 0.001 TRP B 321 HIS 0.002 0.001 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11928) covalent geometry : angle 0.47331 / 0.25 (16266) hydrogen bonds : bond 0.04579 / 2.99 ( 681) hydrogen bonds : angle 3.89646 / 2.75 ( 2007) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 125 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7351 (pp) REVERT: A 330 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6674 (mt) REVERT: B 6 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7101 (pp) REVERT: B 383 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8201 (mp0) REVERT: C 359 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7846 (m-80) REVERT: C 383 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7930 (mp0) outliers start: 55 outliers final: 31 residues processed: 168 average time/residue: 0.0613 time to fit residues: 16.7984 Evaluate side-chains 159 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 318 TRP Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 318 TRP Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 71 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.158647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.142209 restraints weight = 12083.800| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 0.79 r_work: 0.3106 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11928 Z= 0.122 Angle : 0.474 6.810 16266 Z= 0.252 Chirality : 0.037 0.146 1905 Planarity : 0.004 0.035 1944 Dihedral : 5.254 59.762 1584 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.31 % Allowed : 25.12 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.22), residues: 1494 helix: 0.47 (0.16), residues: 1158 sheet: None (None), residues: 0 loop : -1.16 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 296 TYR 0.012 0.001 TYR B 269 PHE 0.014 0.001 PHE B 240 TRP 0.008 0.001 TRP B 140 HIS 0.002 0.001 HIS C 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (11928) covalent geometry : angle 0.47358 / 0.25 (16266) hydrogen bonds : bond 0.04506 / 2.94 ( 681) hydrogen bonds : angle 3.85677 / 2.72 ( 2007) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7381 (pp) REVERT: A 163 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8475 (ttmt) REVERT: A 330 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6282 (mt) REVERT: B 6 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7205 (pp) REVERT: B 40 ASN cc_start: 0.8162 (t0) cc_final: 0.7910 (t0) REVERT: B 163 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8037 (mtmt) REVERT: B 194 MET cc_start: 0.7997 (ttm) cc_final: 0.7509 (mmm) REVERT: B 383 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: C 6 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7580 (pp) REVERT: C 272 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6983 (mp) REVERT: C 359 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7935 (m-80) outliers start: 53 outliers final: 38 residues processed: 167 average time/residue: 0.0581 time to fit residues: 15.7502 Evaluate side-chains 171 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 124 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 318 TRP Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 318 TRP Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 96 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 93 optimal weight: 0.0000 chunk 4 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.160402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.144301 restraints weight = 12026.914| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 0.79 r_work: 0.3240 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work: 0.3082 rms_B_bonded: 4.02 restraints_weight: 0.1250 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11928 Z= 0.110 Angle : 0.452 6.225 16266 Z= 0.240 Chirality : 0.037 0.144 1905 Planarity : 0.004 0.035 1944 Dihedral : 5.090 58.685 1584 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.72 % Allowed : 24.47 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.22), residues: 1494 helix: 0.55 (0.16), residues: 1161 sheet: None (None), residues: 0 loop : -1.07 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 296 TYR 0.010 0.001 TYR B 269 PHE 0.010 0.001 PHE B 240 TRP 0.008 0.001 TRP B 321 HIS 0.002 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (11928) covalent geometry : angle 0.45181 / 0.24 (16266) hydrogen bonds : bond 0.04057 / 2.64 ( 681) hydrogen bonds : angle 3.76089 / 2.65 ( 2007) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 125 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7368 (pp) REVERT: A 330 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6625 (mt) REVERT: B 6 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7165 (pp) REVERT: B 40 ASN cc_start: 0.8457 (t0) cc_final: 0.8245 (t0) REVERT: B 75 PHE cc_start: 0.8110 (m-10) cc_final: 0.7790 (m-10) REVERT: B 163 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8311 (mtmt) REVERT: B 194 MET cc_start: 0.8278 (ttm) cc_final: 0.7779 (mmm) REVERT: B 383 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: C 6 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7435 (pp) REVERT: C 228 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6435 (ttm) REVERT: C 272 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7265 (mp) REVERT: C 359 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.7961 (m-80) outliers start: 58 outliers final: 38 residues processed: 167 average time/residue: 0.0708 time to fit residues: 18.9589 Evaluate side-chains 169 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 318 TRP Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 74 optimal weight: 6.9990 chunk 126 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 56 optimal weight: 0.0000 chunk 80 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.161286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.145843 restraints weight = 12067.696| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 0.78 r_work: 0.3248 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work: 0.3007 rms_B_bonded: 4.89 restraints_weight: 0.1250 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11928 Z= 0.100 Angle : 0.436 5.813 16266 Z= 0.230 Chirality : 0.036 0.147 1905 Planarity : 0.004 0.034 1944 Dihedral : 4.863 56.856 1584 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.07 % Allowed : 24.96 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.22), residues: 1494 helix: 0.61 (0.16), residues: 1173 sheet: None (None), residues: 0 loop : -0.93 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 296 TYR 0.008 0.001 TYR A 269 PHE 0.008 0.001 PHE A 240 TRP 0.010 0.001 TRP B 449 HIS 0.002 0.001 HIS B 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (11928) covalent geometry : angle 0.43631 / 0.23 (16266) hydrogen bonds : bond 0.03644 / 2.37 ( 681) hydrogen bonds : angle 3.66633 / 2.59 ( 2007) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 125 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7634 (pp) REVERT: B 6 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7246 (pp) REVERT: B 75 PHE cc_start: 0.8137 (m-10) cc_final: 0.7798 (m-10) REVERT: B 137 ILE cc_start: 0.8352 (mt) cc_final: 0.8099 (mt) REVERT: B 163 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8464 (mtmt) REVERT: B 194 MET cc_start: 0.8401 (ttm) cc_final: 0.7951 (mmm) REVERT: B 383 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: C 6 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7477 (pp) REVERT: C 126 THR cc_start: 0.9041 (OUTLIER) cc_final: 0.8648 (m) REVERT: C 228 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6466 (ttm) REVERT: C 359 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.7999 (m-80) outliers start: 50 outliers final: 35 residues processed: 159 average time/residue: 0.0685 time to fit residues: 17.6420 Evaluate side-chains 166 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 28 optimal weight: 0.9980 chunk 143 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.157036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.140705 restraints weight = 12042.960| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 0.81 r_work: 0.3142 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11928 Z= 0.163 Angle : 0.524 5.710 16266 Z= 0.278 Chirality : 0.039 0.150 1905 Planarity : 0.004 0.033 1944 Dihedral : 5.190 55.827 1584 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.96 % Allowed : 24.15 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.22), residues: 1494 helix: 0.44 (0.16), residues: 1158 sheet: None (None), residues: 0 loop : -1.16 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 296 TYR 0.016 0.002 TYR B 269 PHE 0.014 0.001 PHE A 240 TRP 0.011 0.001 TRP B 449 HIS 0.003 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (11928) covalent geometry : angle 0.52368 / 0.28 (16266) hydrogen bonds : bond 0.05364 / 3.49 ( 681) hydrogen bonds : angle 3.98563 / 2.79 ( 2007) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 125 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 330 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.6164 (mt) REVERT: B 6 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7219 (pp) REVERT: B 65 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8022 (mp) REVERT: B 163 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8335 (mtmt) REVERT: B 194 MET cc_start: 0.8031 (ttm) cc_final: 0.7524 (mmm) REVERT: B 383 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8135 (mp0) REVERT: C 6 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7529 (pp) REVERT: C 228 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6691 (tpp) REVERT: C 359 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.7906 (m-80) outliers start: 61 outliers final: 47 residues processed: 168 average time/residue: 0.0604 time to fit residues: 16.3442 Evaluate side-chains 179 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 124 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 318 TRP Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 318 TRP Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 0.2980 chunk 94 optimal weight: 7.9990 chunk 146 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.161536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.145189 restraints weight = 11961.272| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 0.76 r_work: 0.3243 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work: 0.3003 rms_B_bonded: 4.56 restraints_weight: 0.1250 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11928 Z= 0.102 Angle : 0.445 5.522 16266 Z= 0.234 Chirality : 0.036 0.150 1905 Planarity : 0.004 0.034 1944 Dihedral : 4.764 51.961 1584 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.31 % Allowed : 24.96 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.22), residues: 1494 helix: 0.60 (0.16), residues: 1173 sheet: None (None), residues: 0 loop : -1.02 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 296 TYR 0.008 0.001 TYR B 269 PHE 0.009 0.001 PHE B 240 TRP 0.011 0.001 TRP B 449 HIS 0.002 0.001 HIS B 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (11928) covalent geometry : angle 0.44471 / 0.23 (16266) hydrogen bonds : bond 0.03721 / 2.43 ( 681) hydrogen bonds : angle 3.70628 / 2.61 ( 2007) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 127 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7363 (pp) REVERT: A 330 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6598 (mt) REVERT: B 6 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7256 (pp) REVERT: B 163 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8469 (mtmt) REVERT: B 194 MET cc_start: 0.8241 (ttm) cc_final: 0.7765 (mmm) REVERT: B 383 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: C 6 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7463 (pp) REVERT: C 228 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6448 (ttm) REVERT: C 359 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.8062 (m-80) outliers start: 53 outliers final: 41 residues processed: 161 average time/residue: 0.0689 time to fit residues: 17.8191 Evaluate side-chains 174 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 125 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 41 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.159666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.142910 restraints weight = 12033.433| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 0.79 r_work: 0.3121 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11928 Z= 0.119 Angle : 0.468 5.530 16266 Z= 0.247 Chirality : 0.037 0.160 1905 Planarity : 0.004 0.034 1944 Dihedral : 4.773 51.286 1584 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.23 % Allowed : 25.12 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.22), residues: 1494 helix: 0.56 (0.16), residues: 1173 sheet: None (None), residues: 0 loop : -1.02 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 296 TYR 0.012 0.001 TYR B 269 PHE 0.011 0.001 PHE A 240 TRP 0.011 0.001 TRP B 449 HIS 0.002 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (11928) covalent geometry : angle 0.46786 / 0.25 (16266) hydrogen bonds : bond 0.04284 / 2.79 ( 681) hydrogen bonds : angle 3.78284 / 2.66 ( 2007) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 124 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7334 (pp) REVERT: B 6 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7306 (pp) REVERT: B 163 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8277 (mtmt) REVERT: B 194 MET cc_start: 0.7894 (ttm) cc_final: 0.7418 (mmm) REVERT: B 383 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: C 6 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7480 (pp) REVERT: C 228 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6540 (tpp) REVERT: C 272 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7060 (mp) REVERT: C 359 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7857 (m-80) outliers start: 52 outliers final: 42 residues processed: 159 average time/residue: 0.0623 time to fit residues: 15.9637 Evaluate side-chains 174 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 124 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 163 LYS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 359 TYR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 469 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 28 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 0.0060 chunk 135 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.162162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.145438 restraints weight = 12047.238| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 0.79 r_work: 0.3242 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work: 0.3067 rms_B_bonded: 4.33 restraints_weight: 0.1250 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11928 Z= 0.097 Angle : 0.435 5.383 16266 Z= 0.228 Chirality : 0.036 0.155 1905 Planarity : 0.004 0.034 1944 Dihedral : 4.501 51.480 1584 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.90 % Allowed : 25.20 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.22), residues: 1494 helix: 0.71 (0.16), residues: 1170 sheet: None (None), residues: 0 loop : -0.98 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 296 TYR 0.007 0.001 TYR C 104 PHE 0.011 0.001 PHE A 75 TRP 0.010 0.001 TRP B 449 HIS 0.003 0.001 HIS B 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (11928) covalent geometry : angle 0.43534 / 0.23 (16266) hydrogen bonds : bond 0.03472 / 2.26 ( 681) hydrogen bonds : angle 3.63199 / 2.56 ( 2007) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2236.06 seconds wall clock time: 38 minutes 54.38 seconds (2334.38 seconds total)