Starting phenix.real_space_refine on Sat Apr 6 05:53:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cye_30498/04_2024/7cye_30498_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cye_30498/04_2024/7cye_30498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cye_30498/04_2024/7cye_30498.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cye_30498/04_2024/7cye_30498.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cye_30498/04_2024/7cye_30498_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cye_30498/04_2024/7cye_30498_neut.pdb" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 39 5.16 5 C 4797 2.51 5 N 1146 2.21 5 O 1281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 162": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 162": "NH1" <-> "NH2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 333": "NH1" <-> "NH2" Residue "B TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 333": "NH1" <-> "NH2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7263 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2421 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 17, 'TRANS': 308} Chain breaks: 1 Chain: "B" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2421 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 17, 'TRANS': 308} Chain breaks: 1 Chain: "C" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2421 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 17, 'TRANS': 308} Chain breaks: 1 Time building chain proxies: 4.43, per 1000 atoms: 0.61 Number of scatterers: 7263 At special positions: 0 Unit cell: (96.235, 100.287, 69.897, 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 39 16.00 O 1281 8.00 N 1146 7.00 C 4797 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.4 seconds 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1764 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 62.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.977A pdb=" N THR A 9 " --> pdb=" O SER A 5 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP A 10 " --> pdb=" O ASN A 6 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.844A pdb=" N LEU A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE A 29 " --> pdb=" O GLY A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 removed outlier: 3.541A pdb=" N THR A 44 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.558A pdb=" N ILE A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 92 removed outlier: 3.522A pdb=" N SER A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU A 80 " --> pdb=" O PHE A 76 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.815A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 144 through 161 removed outlier: 3.549A pdb=" N VAL A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 220 removed outlier: 4.174A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 236 removed outlier: 3.503A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 265 removed outlier: 3.752A pdb=" N SER A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 263 " --> pdb=" O MET A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 removed outlier: 3.576A pdb=" N GLY A 271 " --> pdb=" O TRP A 267 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 276 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 297 Proline residue: A 288 - end of helix removed outlier: 4.382A pdb=" N GLY A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 302 removed outlier: 3.849A pdb=" N ILE A 301 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 302 " --> pdb=" O GLY A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 302' Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.717A pdb=" N VAL A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 359 Processing helix chain 'A' and resid 360 through 371 removed outlier: 3.663A pdb=" N LEU A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 3.976A pdb=" N THR B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B 10 " --> pdb=" O ASN B 6 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY B 13 " --> pdb=" O THR B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 31 removed outlier: 3.844A pdb=" N LEU B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 28 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE B 29 " --> pdb=" O GLY B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 45 removed outlier: 3.542A pdb=" N THR B 44 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.558A pdb=" N ILE B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 92 removed outlier: 3.522A pdb=" N SER B 77 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N VAL B 85 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.815A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 144 through 161 removed outlier: 3.549A pdb=" N VAL B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 150 " --> pdb=" O PRO B 146 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 154 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 220 removed outlier: 4.173A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 236 removed outlier: 3.503A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 265 removed outlier: 3.752A pdb=" N SER B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY B 263 " --> pdb=" O MET B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 277 removed outlier: 3.575A pdb=" N GLY B 271 " --> pdb=" O TRP B 267 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 297 Proline residue: B 288 - end of helix removed outlier: 4.382A pdb=" N GLY B 292 " --> pdb=" O PRO B 288 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.846A pdb=" N ILE B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 302 " --> pdb=" O GLY B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 298 through 302' Processing helix chain 'B' and resid 309 through 318 removed outlier: 3.717A pdb=" N VAL B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL B 315 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 359 Processing helix chain 'B' and resid 360 through 371 removed outlier: 3.663A pdb=" N LEU B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 15 removed outlier: 3.975A pdb=" N THR C 9 " --> pdb=" O SER C 5 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP C 10 " --> pdb=" O ASN C 6 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY C 13 " --> pdb=" O THR C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.844A pdb=" N LEU C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL C 28 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE C 29 " --> pdb=" O GLY C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 45 removed outlier: 3.541A pdb=" N THR C 44 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 64 removed outlier: 3.558A pdb=" N ILE C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG C 63 " --> pdb=" O GLY C 59 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 64 " --> pdb=" O MET C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 92 removed outlier: 3.522A pdb=" N SER C 77 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE C 84 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL C 85 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE C 86 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.815A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 144 through 161 removed outlier: 3.550A pdb=" N VAL C 149 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 150 " --> pdb=" O PRO C 146 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 154 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 220 removed outlier: 4.174A pdb=" N GLU C 217 " --> pdb=" O PRO C 213 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 236 removed outlier: 3.503A pdb=" N LEU C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 265 removed outlier: 3.752A pdb=" N SER C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY C 263 " --> pdb=" O MET C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 277 removed outlier: 3.576A pdb=" N GLY C 271 " --> pdb=" O TRP C 267 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 297 Proline residue: C 288 - end of helix removed outlier: 4.382A pdb=" N GLY C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 295 " --> pdb=" O HIS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 301 removed outlier: 3.831A pdb=" N ILE C 301 " --> pdb=" O LEU C 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 301' Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.717A pdb=" N VAL C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 359 Processing helix chain 'C' and resid 360 through 371 removed outlier: 3.662A pdb=" N LEU C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) 267 hydrogen bonds defined for protein. 756 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: 1.60 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2089 1.34 - 1.45: 1256 1.45 - 1.57: 3996 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 7416 Sorted by residual: bond pdb=" N ILE B 301 " pdb=" CA ILE B 301 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.09e-02 8.42e+03 9.31e+00 bond pdb=" N ILE A 301 " pdb=" CA ILE A 301 " ideal model delta sigma weight residual 1.458 1.492 -0.033 1.22e-02 6.72e+03 7.53e+00 bond pdb=" N TYR B 304 " pdb=" CA TYR B 304 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.16e-02 7.43e+03 6.51e+00 bond pdb=" N THR A 306 " pdb=" CA THR A 306 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.19e+00 bond pdb=" N TYR A 304 " pdb=" CA TYR A 304 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 5.96e+00 ... (remaining 7411 not shown) Histogram of bond angle deviations from ideal: 97.81 - 106.49: 277 106.49 - 115.17: 4443 115.17 - 123.84: 5128 123.84 - 132.52: 237 132.52 - 141.20: 19 Bond angle restraints: 10104 Sorted by residual: angle pdb=" C PHE B 308 " pdb=" N SER B 309 " pdb=" CA SER B 309 " ideal model delta sigma weight residual 121.54 141.20 -19.66 1.91e+00 2.74e-01 1.06e+02 angle pdb=" N ILE C 357 " pdb=" CA ILE C 357 " pdb=" C ILE C 357 " ideal model delta sigma weight residual 113.53 106.04 7.49 9.80e-01 1.04e+00 5.84e+01 angle pdb=" N ILE A 357 " pdb=" CA ILE A 357 " pdb=" C ILE A 357 " ideal model delta sigma weight residual 113.53 106.08 7.45 9.80e-01 1.04e+00 5.79e+01 angle pdb=" N ILE B 357 " pdb=" CA ILE B 357 " pdb=" C ILE B 357 " ideal model delta sigma weight residual 113.53 106.11 7.42 9.80e-01 1.04e+00 5.73e+01 angle pdb=" C GLN C 16 " pdb=" N SER C 17 " pdb=" CA SER C 17 " ideal model delta sigma weight residual 120.68 131.37 -10.69 1.52e+00 4.33e-01 4.94e+01 ... (remaining 10099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.02: 3704 11.02 - 22.03: 422 22.03 - 33.05: 154 33.05 - 44.06: 65 44.06 - 55.08: 14 Dihedral angle restraints: 4359 sinusoidal: 1596 harmonic: 2763 Sorted by residual: dihedral pdb=" CA PRO B 96 " pdb=" C PRO B 96 " pdb=" N ASN B 97 " pdb=" CA ASN B 97 " ideal model delta harmonic sigma weight residual 180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA PRO A 96 " pdb=" C PRO A 96 " pdb=" N ASN A 97 " pdb=" CA ASN A 97 " ideal model delta harmonic sigma weight residual 180.00 -152.06 -27.94 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA PRO C 96 " pdb=" C PRO C 96 " pdb=" N ASN C 97 " pdb=" CA ASN C 97 " ideal model delta harmonic sigma weight residual -180.00 -152.13 -27.87 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 4356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1037 0.088 - 0.176: 193 0.176 - 0.264: 12 0.264 - 0.352: 3 0.352 - 0.441: 3 Chirality restraints: 1248 Sorted by residual: chirality pdb=" CB ILE A 361 " pdb=" CA ILE A 361 " pdb=" CG1 ILE A 361 " pdb=" CG2 ILE A 361 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.85e+00 chirality pdb=" CB ILE C 361 " pdb=" CA ILE C 361 " pdb=" CG1 ILE C 361 " pdb=" CG2 ILE C 361 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.84e+00 chirality pdb=" CB ILE B 361 " pdb=" CA ILE B 361 " pdb=" CG1 ILE B 361 " pdb=" CG2 ILE B 361 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.81e+00 ... (remaining 1245 not shown) Planarity restraints: 1236 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 329 " 0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO C 330 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO C 330 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 330 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 329 " -0.055 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO B 330 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 330 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 330 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 329 " 0.055 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 330 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " 0.047 5.00e-02 4.00e+02 ... (remaining 1233 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1459 2.77 - 3.30: 6805 3.30 - 3.83: 11453 3.83 - 4.37: 13588 4.37 - 4.90: 23044 Nonbonded interactions: 56349 Sorted by model distance: nonbonded pdb=" O SER C 309 " pdb=" N GLY C 312 " model vdw 2.232 2.520 nonbonded pdb=" O SER A 43 " pdb=" OG SER A 43 " model vdw 2.397 2.440 nonbonded pdb=" O SER B 43 " pdb=" OG SER B 43 " model vdw 2.398 2.440 nonbonded pdb=" O SER C 43 " pdb=" OG SER C 43 " model vdw 2.399 2.440 nonbonded pdb=" CZ PHE B 308 " pdb=" O GLY B 312 " model vdw 2.414 3.340 ... (remaining 56344 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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 group one per residue 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: 0.560 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: 2.140 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 22.260 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 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 : 0.010 0.078 7416 Z= 0.624 Angle : 1.423 19.656 10104 Z= 0.759 Chirality : 0.071 0.441 1248 Planarity : 0.010 0.083 1236 Dihedral : 12.312 55.076 2595 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.62 % Allowed : 12.42 % Favored : 86.96 % Rotamer: Outliers : 1.30 % Allowed : 8.98 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.38 (0.15), residues: 966 helix: -4.67 (0.08), residues: 663 sheet: None (None), residues: 0 loop : -4.90 (0.27), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 267 HIS 0.003 0.001 HIS B 291 PHE 0.045 0.004 PHE B 22 TYR 0.016 0.003 TYR B 132 ARG 0.006 0.001 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 258 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 SER cc_start: 0.8888 (t) cc_final: 0.8587 (m) REVERT: A 92 LEU cc_start: 0.7902 (tp) cc_final: 0.7657 (tt) REVERT: A 104 LEU cc_start: 0.8688 (tt) cc_final: 0.8479 (tt) REVERT: A 212 TRP cc_start: 0.5837 (t60) cc_final: 0.5250 (t-100) REVERT: B 1 MET cc_start: 0.2230 (tmt) cc_final: 0.1913 (mtt) REVERT: B 57 THR cc_start: 0.8349 (m) cc_final: 0.8122 (p) REVERT: B 274 ARG cc_start: 0.6893 (mtt180) cc_final: 0.6467 (mmt180) REVERT: B 298 LEU cc_start: 0.8440 (tm) cc_final: 0.8145 (tp) REVERT: C 10 ASP cc_start: 0.7861 (t0) cc_final: 0.7489 (t70) REVERT: C 66 ASN cc_start: 0.7153 (p0) cc_final: 0.6714 (p0) REVERT: C 79 ILE cc_start: 0.9154 (mm) cc_final: 0.8954 (mp) REVERT: C 135 TRP cc_start: 0.7974 (p90) cc_final: 0.7697 (p90) REVERT: C 157 ILE cc_start: 0.8380 (tt) cc_final: 0.8130 (tt) REVERT: C 272 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7608 (tm-30) outliers start: 10 outliers final: 1 residues processed: 264 average time/residue: 0.1789 time to fit residues: 63.2837 Evaluate side-chains 186 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 0.0030 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 GLN A 291 HIS A 340 ASN B 291 HIS C 160 ASN C 291 HIS C 303 HIS C 340 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 7416 Z= 0.219 Angle : 0.868 14.177 10104 Z= 0.427 Chirality : 0.046 0.291 1248 Planarity : 0.007 0.070 1236 Dihedral : 6.595 37.449 1028 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 5.47 % Allowed : 15.10 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.72 (0.20), residues: 966 helix: -3.41 (0.15), residues: 642 sheet: None (None), residues: 0 loop : -4.28 (0.28), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 135 HIS 0.001 0.000 HIS A 303 PHE 0.026 0.001 PHE C 364 TYR 0.013 0.001 TYR B 132 ARG 0.007 0.001 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 194 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.6997 (p) REVERT: A 77 SER cc_start: 0.8811 (t) cc_final: 0.8532 (m) REVERT: A 92 LEU cc_start: 0.8084 (tp) cc_final: 0.7883 (tt) REVERT: A 104 LEU cc_start: 0.8698 (tt) cc_final: 0.8358 (tt) REVERT: A 162 ARG cc_start: 0.7710 (tpt90) cc_final: 0.7466 (tpt90) REVERT: B 44 THR cc_start: 0.9067 (t) cc_final: 0.8585 (m) REVERT: B 70 MET cc_start: 0.8635 (ttm) cc_final: 0.8336 (ttm) REVERT: B 250 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7911 (pp) REVERT: B 274 ARG cc_start: 0.6979 (mtt180) cc_final: 0.6561 (mmt180) REVERT: B 298 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8053 (tp) REVERT: C 10 ASP cc_start: 0.7623 (t0) cc_final: 0.7245 (t70) REVERT: C 24 ILE cc_start: 0.8553 (pp) cc_final: 0.8344 (mm) REVERT: C 90 PHE cc_start: 0.6184 (m-10) cc_final: 0.5678 (m-80) REVERT: C 135 TRP cc_start: 0.8071 (p90) cc_final: 0.7831 (p90) REVERT: C 258 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6993 (tp) REVERT: C 272 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7651 (tm-30) REVERT: C 300 MET cc_start: 0.8603 (mmt) cc_final: 0.8369 (mmm) outliers start: 42 outliers final: 21 residues processed: 221 average time/residue: 0.1607 time to fit residues: 49.6137 Evaluate side-chains 201 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 176 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 220 GLN Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 370 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 86 optimal weight: 6.9990 chunk 29 optimal weight: 0.0050 chunk 70 optimal weight: 0.0570 overall best weight: 0.6514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 160 ASN A 220 GLN C 291 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7416 Z= 0.188 Angle : 0.796 12.012 10104 Z= 0.382 Chirality : 0.043 0.178 1248 Planarity : 0.006 0.069 1236 Dihedral : 5.784 21.686 1026 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 4.69 % Allowed : 18.49 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.81 (0.22), residues: 966 helix: -2.48 (0.18), residues: 615 sheet: None (None), residues: 0 loop : -4.41 (0.25), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 135 HIS 0.004 0.001 HIS C 291 PHE 0.012 0.001 PHE B 308 TYR 0.007 0.001 TYR A 132 ARG 0.004 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 190 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7947 (tm-30) REVERT: A 68 THR cc_start: 0.7530 (t) cc_final: 0.7052 (p) REVERT: A 77 SER cc_start: 0.8839 (t) cc_final: 0.8599 (m) REVERT: A 259 MET cc_start: 0.7655 (ttm) cc_final: 0.7266 (ttm) REVERT: B 1 MET cc_start: 0.3827 (mmm) cc_final: 0.3574 (mmm) REVERT: B 44 THR cc_start: 0.9127 (t) cc_final: 0.8795 (m) REVERT: B 274 ARG cc_start: 0.6830 (mtt180) cc_final: 0.6413 (mmt180) REVERT: B 298 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7975 (tp) REVERT: C 10 ASP cc_start: 0.7595 (t0) cc_final: 0.7204 (t70) REVERT: C 90 PHE cc_start: 0.6137 (m-10) cc_final: 0.5569 (m-10) REVERT: C 212 TRP cc_start: 0.6605 (t60) cc_final: 0.5634 (t-100) REVERT: C 248 ASP cc_start: 0.7720 (t0) cc_final: 0.6847 (m-30) REVERT: C 272 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7661 (tm-30) REVERT: C 300 MET cc_start: 0.8631 (mmt) cc_final: 0.8356 (mmm) outliers start: 36 outliers final: 19 residues processed: 213 average time/residue: 0.1584 time to fit residues: 47.7617 Evaluate side-chains 197 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 331 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 30.0000 chunk 41 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 0.0000 chunk 25 optimal weight: 0.0970 chunk 77 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN C 291 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7416 Z= 0.213 Angle : 0.816 13.507 10104 Z= 0.382 Chirality : 0.044 0.167 1248 Planarity : 0.006 0.065 1236 Dihedral : 5.416 22.549 1026 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 5.34 % Allowed : 19.27 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.26 (0.24), residues: 966 helix: -1.97 (0.19), residues: 651 sheet: None (None), residues: 0 loop : -4.54 (0.26), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP C 135 HIS 0.002 0.000 HIS C 291 PHE 0.026 0.001 PHE C 7 TYR 0.011 0.001 TYR A 158 ARG 0.002 0.000 ARG A 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 68 THR cc_start: 0.7761 (OUTLIER) cc_final: 0.7334 (p) REVERT: A 77 SER cc_start: 0.8923 (t) cc_final: 0.8590 (m) REVERT: A 156 ASN cc_start: 0.8099 (OUTLIER) cc_final: 0.7782 (m-40) REVERT: A 272 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7643 (tm-30) REVERT: B 159 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8067 (mt) REVERT: B 274 ARG cc_start: 0.6849 (mtt180) cc_final: 0.6436 (mmt180) REVERT: B 298 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7844 (tp) REVERT: C 10 ASP cc_start: 0.7710 (t0) cc_final: 0.7270 (t70) REVERT: C 90 PHE cc_start: 0.6238 (m-10) cc_final: 0.5852 (m-10) REVERT: C 212 TRP cc_start: 0.6478 (t60) cc_final: 0.5631 (t-100) REVERT: C 272 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7682 (tm-30) outliers start: 41 outliers final: 24 residues processed: 215 average time/residue: 0.1680 time to fit residues: 49.9842 Evaluate side-chains 200 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 370 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN C 291 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 7416 Z= 0.319 Angle : 0.868 12.221 10104 Z= 0.409 Chirality : 0.046 0.168 1248 Planarity : 0.006 0.069 1236 Dihedral : 5.676 21.857 1026 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 5.73 % Allowed : 21.35 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.24), residues: 966 helix: -1.78 (0.20), residues: 621 sheet: None (None), residues: 0 loop : -4.07 (0.27), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 135 HIS 0.002 0.000 HIS B 303 PHE 0.016 0.002 PHE B 22 TYR 0.011 0.002 TYR B 280 ARG 0.005 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 195 time to evaluate : 0.752 Fit side-chains REVERT: A 68 THR cc_start: 0.7950 (OUTLIER) cc_final: 0.7579 (p) REVERT: A 77 SER cc_start: 0.8981 (t) cc_final: 0.8546 (m) REVERT: A 156 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7847 (m-40) REVERT: A 240 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8203 (mm-30) REVERT: A 250 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8257 (pp) REVERT: A 259 MET cc_start: 0.7631 (ttm) cc_final: 0.7179 (ttm) REVERT: A 272 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7764 (tm-30) REVERT: B 60 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8823 (mtm) REVERT: B 132 TYR cc_start: 0.7949 (p90) cc_final: 0.7664 (p90) REVERT: B 159 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8092 (mt) REVERT: B 258 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7515 (tm) REVERT: B 264 MET cc_start: 0.8206 (ptm) cc_final: 0.7955 (ptp) REVERT: B 274 ARG cc_start: 0.6924 (mtt180) cc_final: 0.6438 (mmt180) REVERT: C 90 PHE cc_start: 0.6459 (m-10) cc_final: 0.6039 (m-10) REVERT: C 272 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7714 (tm-30) REVERT: C 274 ARG cc_start: 0.7189 (mtt180) cc_final: 0.6740 (mmt180) outliers start: 44 outliers final: 28 residues processed: 218 average time/residue: 0.1665 time to fit residues: 50.0095 Evaluate side-chains 212 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 178 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 370 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 77 optimal weight: 0.2980 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN A 160 ASN C 291 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7416 Z= 0.188 Angle : 0.791 12.404 10104 Z= 0.366 Chirality : 0.043 0.179 1248 Planarity : 0.006 0.067 1236 Dihedral : 5.251 20.573 1026 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 3.91 % Allowed : 24.09 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.25), residues: 966 helix: -1.41 (0.21), residues: 633 sheet: None (None), residues: 0 loop : -4.43 (0.24), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 135 HIS 0.001 0.000 HIS C 291 PHE 0.013 0.001 PHE C 7 TYR 0.014 0.001 TYR A 158 ARG 0.002 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 0.714 Fit side-chains REVERT: A 60 MET cc_start: 0.8622 (mtt) cc_final: 0.8063 (mtm) REVERT: A 77 SER cc_start: 0.8944 (t) cc_final: 0.8575 (m) REVERT: A 156 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7869 (m-40) REVERT: A 219 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9041 (tt) REVERT: A 250 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8137 (pp) REVERT: A 272 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7724 (tm-30) REVERT: B 60 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8358 (mtm) REVERT: B 250 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8162 (pp) REVERT: B 274 ARG cc_start: 0.6915 (mtt180) cc_final: 0.6458 (mmt180) REVERT: C 90 PHE cc_start: 0.6466 (m-10) cc_final: 0.6059 (m-10) REVERT: C 272 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7739 (tm-30) REVERT: C 274 ARG cc_start: 0.7118 (mtt180) cc_final: 0.6673 (mmt180) outliers start: 30 outliers final: 17 residues processed: 199 average time/residue: 0.1629 time to fit residues: 45.1608 Evaluate side-chains 196 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 42 optimal weight: 0.3980 chunk 36 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7416 Z= 0.189 Angle : 0.781 12.766 10104 Z= 0.361 Chirality : 0.043 0.147 1248 Planarity : 0.005 0.066 1236 Dihedral : 5.030 20.369 1026 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 5.08 % Allowed : 22.79 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.26), residues: 966 helix: -1.17 (0.21), residues: 630 sheet: None (None), residues: 0 loop : -4.34 (0.25), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 135 HIS 0.001 0.000 HIS C 291 PHE 0.022 0.001 PHE B 308 TYR 0.007 0.001 TYR B 132 ARG 0.001 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 181 time to evaluate : 0.825 Fit side-chains REVERT: A 77 SER cc_start: 0.8944 (t) cc_final: 0.8580 (m) REVERT: A 250 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8144 (pp) REVERT: A 272 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7785 (tm-30) REVERT: B 60 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8579 (mtm) REVERT: B 250 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8150 (pp) REVERT: B 274 ARG cc_start: 0.6919 (mtt180) cc_final: 0.6477 (mmt180) REVERT: C 90 PHE cc_start: 0.6514 (m-10) cc_final: 0.6112 (m-10) REVERT: C 240 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8118 (mm-30) REVERT: C 274 ARG cc_start: 0.7129 (mtt180) cc_final: 0.6620 (mmt180) outliers start: 39 outliers final: 24 residues processed: 202 average time/residue: 0.1616 time to fit residues: 45.9197 Evaluate side-chains 197 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 370 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 0.0470 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 0.0000 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 0.1980 chunk 80 optimal weight: 5.9990 overall best weight: 0.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7416 Z= 0.161 Angle : 0.767 12.134 10104 Z= 0.349 Chirality : 0.042 0.138 1248 Planarity : 0.005 0.064 1236 Dihedral : 4.818 20.567 1026 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 2.99 % Allowed : 24.74 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.26), residues: 966 helix: -0.86 (0.22), residues: 624 sheet: None (None), residues: 0 loop : -4.24 (0.25), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 135 HIS 0.001 0.000 HIS C 291 PHE 0.013 0.001 PHE C 7 TYR 0.010 0.001 TYR A 158 ARG 0.005 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 0.790 Fit side-chains REVERT: A 77 SER cc_start: 0.8817 (t) cc_final: 0.8463 (m) REVERT: A 90 PHE cc_start: 0.6487 (m-80) cc_final: 0.6224 (m-80) REVERT: A 144 ASP cc_start: 0.8200 (t0) cc_final: 0.7962 (t0) REVERT: A 250 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8022 (pp) REVERT: A 272 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7775 (tm-30) REVERT: B 60 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8608 (mtm) REVERT: B 250 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7985 (pp) REVERT: B 274 ARG cc_start: 0.6826 (mtt180) cc_final: 0.6441 (mmt180) REVERT: C 86 PHE cc_start: 0.8214 (m-80) cc_final: 0.7881 (m-80) REVERT: C 90 PHE cc_start: 0.6614 (m-10) cc_final: 0.6230 (m-10) REVERT: C 95 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7569 (mp) REVERT: C 212 TRP cc_start: 0.6480 (t60) cc_final: 0.5791 (t-100) outliers start: 23 outliers final: 15 residues processed: 186 average time/residue: 0.1516 time to fit residues: 39.9158 Evaluate side-chains 185 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 166 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 359 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 77 optimal weight: 0.1980 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7416 Z= 0.167 Angle : 0.758 13.221 10104 Z= 0.346 Chirality : 0.043 0.177 1248 Planarity : 0.005 0.064 1236 Dihedral : 4.707 20.168 1026 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 2.86 % Allowed : 25.00 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.26), residues: 966 helix: -0.75 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -4.12 (0.24), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 135 HIS 0.001 0.000 HIS C 303 PHE 0.011 0.001 PHE C 7 TYR 0.005 0.001 TYR C 132 ARG 0.006 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 171 time to evaluate : 0.797 Fit side-chains REVERT: A 77 SER cc_start: 0.8899 (t) cc_final: 0.8528 (m) REVERT: A 90 PHE cc_start: 0.6506 (m-80) cc_final: 0.6256 (m-80) REVERT: A 250 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8025 (pp) REVERT: A 272 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7780 (tm-30) REVERT: B 60 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8499 (mtm) REVERT: B 250 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8007 (pp) REVERT: B 274 ARG cc_start: 0.6882 (mtt180) cc_final: 0.6430 (mmt180) REVERT: C 86 PHE cc_start: 0.8146 (m-80) cc_final: 0.7771 (m-80) REVERT: C 90 PHE cc_start: 0.6708 (m-10) cc_final: 0.6329 (m-10) REVERT: C 212 TRP cc_start: 0.6467 (t60) cc_final: 0.5803 (t-100) outliers start: 22 outliers final: 16 residues processed: 181 average time/residue: 0.1493 time to fit residues: 38.3479 Evaluate side-chains 180 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 359 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.6299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7416 Z= 0.175 Angle : 0.771 13.417 10104 Z= 0.351 Chirality : 0.042 0.132 1248 Planarity : 0.005 0.063 1236 Dihedral : 4.667 19.392 1026 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 2.73 % Allowed : 25.91 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.26), residues: 966 helix: -0.61 (0.22), residues: 606 sheet: None (None), residues: 0 loop : -4.09 (0.25), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 135 HIS 0.001 0.000 HIS C 291 PHE 0.011 0.001 PHE C 7 TYR 0.005 0.001 TYR C 140 ARG 0.008 0.000 ARG A 89 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 0.705 Fit side-chains REVERT: A 90 PHE cc_start: 0.6564 (m-80) cc_final: 0.6283 (m-80) REVERT: A 250 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7969 (pp) REVERT: A 272 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7800 (tm-30) REVERT: B 60 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8475 (mtm) REVERT: B 250 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8059 (pp) REVERT: B 274 ARG cc_start: 0.6896 (mtt180) cc_final: 0.6417 (mmt180) REVERT: C 86 PHE cc_start: 0.8117 (m-80) cc_final: 0.7737 (m-80) REVERT: C 90 PHE cc_start: 0.6721 (m-10) cc_final: 0.6354 (m-10) REVERT: C 212 TRP cc_start: 0.6571 (t60) cc_final: 0.5940 (t-100) outliers start: 21 outliers final: 17 residues processed: 176 average time/residue: 0.1661 time to fit residues: 41.7015 Evaluate side-chains 186 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 359 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.0050 chunk 11 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.152243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116639 restraints weight = 10644.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119832 restraints weight = 6266.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121741 restraints weight = 4592.699| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.6409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7416 Z= 0.167 Angle : 0.772 13.079 10104 Z= 0.349 Chirality : 0.042 0.166 1248 Planarity : 0.005 0.063 1236 Dihedral : 4.570 19.429 1026 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 2.73 % Allowed : 25.52 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.27), residues: 966 helix: -0.37 (0.22), residues: 609 sheet: None (None), residues: 0 loop : -3.88 (0.25), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 135 HIS 0.001 0.000 HIS C 291 PHE 0.011 0.001 PHE C 7 TYR 0.007 0.001 TYR C 132 ARG 0.008 0.000 ARG A 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1730.95 seconds wall clock time: 32 minutes 19.37 seconds (1939.37 seconds total)