Starting phenix.real_space_refine on Thu Jul 31 09:42:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cju_7484/07_2025/6cju_7484.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cju_7484/07_2025/6cju_7484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6cju_7484/07_2025/6cju_7484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cju_7484/07_2025/6cju_7484.map" model { file = "/net/cci-nas-00/data/ceres_data/6cju_7484/07_2025/6cju_7484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cju_7484/07_2025/6cju_7484.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 28 5.16 5 C 8704 2.51 5 N 2080 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13076 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3102 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 24, 'TRANS': 365} Chain breaks: 1 Chain: "A" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 167 Unusual residues: {'PGW': 8} Classifications: {'RNA': 1, 'undetermined': 8} Modifications used: {'rna3p': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 309 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PGW:plan-1': 6, 'PGW:plan-2': 6, 'PGW:plan-3': 7} Unresolved non-hydrogen planarities: 61 Restraints were copied for chains: C, B, D Time building chain proxies: 6.88, per 1000 atoms: 0.53 Number of scatterers: 13076 At special positions: 0 Unit cell: (106.252, 106.252, 120.204, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 8 15.00 O 2256 8.00 N 2080 7.00 C 8704 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: 3.01 Conformation dependent library (CDL) restraints added in 1.6 seconds 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 66.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 10 through 35 removed outlier: 4.436A pdb=" N VAL A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TRP A 15 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 3.760A pdb=" N VAL A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 62 removed outlier: 6.360A pdb=" N LEU A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 4.324A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 91 through 98 removed outlier: 4.697A pdb=" N VAL A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 104 No H-bonds generated for 'chain 'A' and resid 103 through 104' Processing helix chain 'A' and resid 105 through 114 removed outlier: 4.091A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 removed outlier: 4.057A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 158 removed outlier: 3.535A pdb=" N ARG A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 181 removed outlier: 4.040A pdb=" N TYR A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 224 removed outlier: 3.811A pdb=" N TYR A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.862A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.767A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.707A pdb=" N LEU A 276 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 278' Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 293 through 298 removed outlier: 4.031A pdb=" N GLU A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LYS A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 298' Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.637A pdb=" N ARG A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N HIS A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 4.574A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'A' and resid 394 through 403 removed outlier: 3.592A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 removed outlier: 4.348A pdb=" N GLN A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 35 removed outlier: 4.436A pdb=" N VAL B 14 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TRP B 15 " --> pdb=" O TYR B 11 " (cutoff:3.500A) Proline residue: B 31 - end of helix removed outlier: 3.760A pdb=" N VAL B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 62 removed outlier: 6.360A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Proline residue: B 45 - end of helix removed outlier: 4.324A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 91 through 98 removed outlier: 4.697A pdb=" N VAL B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE B 96 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 104 No H-bonds generated for 'chain 'B' and resid 103 through 104' Processing helix chain 'B' and resid 105 through 114 removed outlier: 4.091A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 126 removed outlier: 4.057A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 158 removed outlier: 3.535A pdb=" N ARG B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 removed outlier: 4.040A pdb=" N TYR B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 224 removed outlier: 3.811A pdb=" N TYR B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 245 removed outlier: 3.862A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.767A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 278 removed outlier: 3.707A pdb=" N LEU B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 272 through 278' Processing helix chain 'B' and resid 281 through 292 Processing helix chain 'B' and resid 293 through 298 removed outlier: 4.031A pdb=" N GLU B 297 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LYS B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 293 through 298' Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.637A pdb=" N ARG B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N HIS B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 4.574A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU B 373 " --> pdb=" O MET B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 394 through 403 removed outlier: 3.592A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 removed outlier: 4.348A pdb=" N GLN B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 35 removed outlier: 4.436A pdb=" N VAL C 14 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TRP C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) Proline residue: C 31 - end of helix removed outlier: 3.760A pdb=" N VAL C 35 " --> pdb=" O PRO C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 62 removed outlier: 6.360A pdb=" N LEU C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Proline residue: C 45 - end of helix removed outlier: 4.324A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 91 through 98 removed outlier: 4.697A pdb=" N VAL C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 104 No H-bonds generated for 'chain 'C' and resid 103 through 104' Processing helix chain 'C' and resid 105 through 114 removed outlier: 4.091A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 126 removed outlier: 4.057A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 158 removed outlier: 3.535A pdb=" N ARG C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 181 removed outlier: 4.040A pdb=" N TYR C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 181 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 224 removed outlier: 3.811A pdb=" N TYR C 199 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 245 removed outlier: 3.862A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.767A pdb=" N ARG C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 278 removed outlier: 3.707A pdb=" N LEU C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS C 277 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 278' Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 293 through 298 removed outlier: 4.031A pdb=" N GLU C 297 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LYS C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 293 through 298' Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.637A pdb=" N ARG C 311 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N HIS C 316 " --> pdb=" O ASP C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 4.574A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU C 373 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 394 through 403 removed outlier: 3.592A pdb=" N SER C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 removed outlier: 4.348A pdb=" N GLN C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 35 removed outlier: 4.436A pdb=" N VAL D 14 " --> pdb=" O THR D 10 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TRP D 15 " --> pdb=" O TYR D 11 " (cutoff:3.500A) Proline residue: D 31 - end of helix removed outlier: 3.760A pdb=" N VAL D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 62 removed outlier: 6.360A pdb=" N LEU D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Proline residue: D 45 - end of helix removed outlier: 4.324A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 91 through 98 removed outlier: 4.697A pdb=" N VAL D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE D 96 " --> pdb=" O ASP D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 104 No H-bonds generated for 'chain 'D' and resid 103 through 104' Processing helix chain 'D' and resid 105 through 114 removed outlier: 4.091A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 126 removed outlier: 4.057A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 158 removed outlier: 3.535A pdb=" N ARG D 136 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 181 removed outlier: 4.040A pdb=" N TYR D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU D 181 " --> pdb=" O THR D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 224 removed outlier: 3.811A pdb=" N TYR D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.862A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.767A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 278 removed outlier: 3.707A pdb=" N LEU D 276 " --> pdb=" O GLU D 272 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS D 277 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 272 through 278' Processing helix chain 'D' and resid 281 through 292 Processing helix chain 'D' and resid 293 through 298 removed outlier: 4.031A pdb=" N GLU D 297 " --> pdb=" O GLY D 293 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LYS D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 293 through 298' Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.637A pdb=" N ARG D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N HIS D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 4.574A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU D 373 " --> pdb=" O MET D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 373' Processing helix chain 'D' and resid 394 through 403 removed outlier: 3.592A pdb=" N SER D 402 " --> pdb=" O ASP D 398 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 412 removed outlier: 4.348A pdb=" N GLN D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1608 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: 3.18 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2444 1.33 - 1.44: 2976 1.44 - 1.56: 7856 1.56 - 1.68: 12 1.68 - 1.80: 52 Bond restraints: 13340 Sorted by residual: bond pdb=" O12 PGW B 501 " pdb=" P PGW B 501 " ideal model delta sigma weight residual 1.636 1.693 -0.057 2.00e-02 2.50e+03 8.04e+00 bond pdb=" O12 PGW C 501 " pdb=" P PGW C 501 " ideal model delta sigma weight residual 1.636 1.693 -0.057 2.00e-02 2.50e+03 8.04e+00 bond pdb=" O12 PGW D 501 " pdb=" P PGW D 501 " ideal model delta sigma weight residual 1.636 1.693 -0.057 2.00e-02 2.50e+03 8.04e+00 bond pdb=" O12 PGW A 501 " pdb=" P PGW A 501 " ideal model delta sigma weight residual 1.636 1.693 -0.057 2.00e-02 2.50e+03 8.04e+00 bond pdb=" C03 PGW D 501 " pdb=" O11 PGW D 501 " ideal model delta sigma weight residual 1.412 1.363 0.049 2.00e-02 2.50e+03 6.11e+00 ... (remaining 13335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 16168 2.05 - 4.10: 1280 4.10 - 6.16: 332 6.16 - 8.21: 184 8.21 - 10.26: 48 Bond angle restraints: 18012 Sorted by residual: angle pdb=" C4' CMP A 500 " pdb=" C3' CMP A 500 " pdb=" O3' CMP A 500 " ideal model delta sigma weight residual 113.00 104.61 8.39 1.50e+00 4.44e-01 3.13e+01 angle pdb=" C4' CMP B 500 " pdb=" C3' CMP B 500 " pdb=" O3' CMP B 500 " ideal model delta sigma weight residual 113.00 104.61 8.39 1.50e+00 4.44e-01 3.13e+01 angle pdb=" C4' CMP D 500 " pdb=" C3' CMP D 500 " pdb=" O3' CMP D 500 " ideal model delta sigma weight residual 113.00 104.61 8.39 1.50e+00 4.44e-01 3.13e+01 angle pdb=" C4' CMP C 500 " pdb=" C3' CMP C 500 " pdb=" O3' CMP C 500 " ideal model delta sigma weight residual 113.00 104.61 8.39 1.50e+00 4.44e-01 3.13e+01 angle pdb=" C ASP D 92 " pdb=" N LEU D 93 " pdb=" CA LEU D 93 " ideal model delta sigma weight residual 121.54 131.80 -10.26 1.91e+00 2.74e-01 2.88e+01 ... (remaining 18007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 7924 34.88 - 69.76: 180 69.76 - 104.64: 24 104.64 - 139.52: 24 139.52 - 174.39: 16 Dihedral angle restraints: 8168 sinusoidal: 3580 harmonic: 4588 Sorted by residual: dihedral pdb=" C3' CMP A 500 " pdb=" O3' CMP A 500 " pdb=" P CMP A 500 " pdb=" O1P CMP A 500 " ideal model delta sinusoidal sigma weight residual -60.00 114.29 -174.29 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3' CMP B 500 " pdb=" O3' CMP B 500 " pdb=" P CMP B 500 " pdb=" O1P CMP B 500 " ideal model delta sinusoidal sigma weight residual -60.00 114.29 -174.29 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3' CMP D 500 " pdb=" O3' CMP D 500 " pdb=" P CMP D 500 " pdb=" O1P CMP D 500 " ideal model delta sinusoidal sigma weight residual -60.00 114.29 -174.29 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 8165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1740 0.092 - 0.185: 324 0.185 - 0.277: 24 0.277 - 0.369: 4 0.369 - 0.461: 4 Chirality restraints: 2096 Sorted by residual: chirality pdb=" CB ILE D 58 " pdb=" CA ILE D 58 " pdb=" CG1 ILE D 58 " pdb=" CG2 ILE D 58 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" CB ILE C 58 " pdb=" CA ILE C 58 " pdb=" CG1 ILE C 58 " pdb=" CG2 ILE C 58 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" CB ILE B 58 " pdb=" CA ILE B 58 " pdb=" CG1 ILE B 58 " pdb=" CG2 ILE B 58 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.32e+00 ... (remaining 2093 not shown) Planarity restraints: 2164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 93 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C LEU C 93 " -0.064 2.00e-02 2.50e+03 pdb=" O LEU C 93 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU C 94 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 93 " 0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C LEU B 93 " -0.064 2.00e-02 2.50e+03 pdb=" O LEU B 93 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU B 94 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 93 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.35e+01 pdb=" C LEU D 93 " 0.064 2.00e-02 2.50e+03 pdb=" O LEU D 93 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU D 94 " -0.021 2.00e-02 2.50e+03 ... (remaining 2161 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3328 2.80 - 3.33: 11372 3.33 - 3.85: 20892 3.85 - 4.38: 23112 4.38 - 4.90: 41884 Nonbonded interactions: 100588 Sorted by model distance: nonbonded pdb=" OH TYR B 175 " pdb=" OD2 ASP B 188 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR C 175 " pdb=" OD2 ASP C 188 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR A 175 " pdb=" OD2 ASP A 188 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR D 175 " pdb=" OD2 ASP D 188 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.322 3.040 ... (remaining 100583 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 1.360 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 28.480 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.011 0.079 13340 Z= 0.457 Angle : 1.507 10.258 18012 Z= 0.715 Chirality : 0.071 0.461 2096 Planarity : 0.009 0.058 2164 Dihedral : 18.925 174.394 5208 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.49 % Allowed : 6.87 % Favored : 91.64 % 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: -4.12 (0.17), residues: 1544 helix: -2.63 (0.13), residues: 888 sheet: -1.79 (0.46), residues: 92 loop : -2.79 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 264 HIS 0.006 0.002 HIS B 292 PHE 0.014 0.003 PHE A 365 TYR 0.026 0.004 TYR A 211 ARG 0.005 0.001 ARG C 124 Details of bonding type rmsd hydrogen bonds : bond 0.10497 ( 560) hydrogen bonds : angle 6.00402 ( 1608) covalent geometry : bond 0.01075 (13340) covalent geometry : angle 1.50713 (18012) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 1.382 Fit side-chains REVERT: B 171 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8558 (tp) REVERT: B 233 ARG cc_start: 0.8393 (ttt90) cc_final: 0.8013 (mtp85) REVERT: D 229 LYS cc_start: 0.9054 (tmtp) cc_final: 0.8847 (tttp) outliers start: 20 outliers final: 3 residues processed: 248 average time/residue: 0.3264 time to fit residues: 108.4051 Evaluate side-chains 121 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 171 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 122 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 GLN ** 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 = 0.3739 r_free = 0.3739 target = 0.147364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114544 restraints weight = 17291.816| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.64 r_work: 0.2964 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13340 Z= 0.137 Angle : 0.718 7.388 18012 Z= 0.339 Chirality : 0.043 0.227 2096 Planarity : 0.006 0.040 2164 Dihedral : 21.576 167.011 2268 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.66 % Allowed : 12.91 % Favored : 83.43 % 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: -1.98 (0.21), residues: 1544 helix: -0.60 (0.17), residues: 888 sheet: -1.40 (0.49), residues: 92 loop : -2.35 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 264 HIS 0.002 0.001 HIS D 149 PHE 0.009 0.001 PHE D 302 TYR 0.014 0.001 TYR B 128 ARG 0.004 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 560) hydrogen bonds : angle 4.12650 ( 1608) covalent geometry : bond 0.00313 (13340) covalent geometry : angle 0.71760 (18012) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 1.425 Fit side-chains REVERT: A 126 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.6897 (pp) REVERT: A 233 ARG cc_start: 0.8535 (ttt90) cc_final: 0.8227 (mtp85) REVERT: A 272 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7756 (tp30) REVERT: A 318 GLU cc_start: 0.8338 (tt0) cc_final: 0.7999 (mt-10) REVERT: B 126 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6698 (pp) REVERT: B 233 ARG cc_start: 0.8525 (ttt90) cc_final: 0.8233 (mtp85) REVERT: B 272 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7788 (tp30) REVERT: B 318 GLU cc_start: 0.8326 (tt0) cc_final: 0.7986 (mt-10) REVERT: C 114 LYS cc_start: 0.8402 (tptp) cc_final: 0.8050 (tttp) REVERT: C 126 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6810 (pp) REVERT: C 171 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8520 (tp) REVERT: C 233 ARG cc_start: 0.8379 (ttt90) cc_final: 0.8106 (mtp85) REVERT: C 272 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7779 (tp30) REVERT: C 318 GLU cc_start: 0.8303 (tt0) cc_final: 0.7996 (mt-10) REVERT: D 126 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6729 (pp) REVERT: D 171 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8526 (tp) REVERT: D 233 ARG cc_start: 0.8398 (ttt90) cc_final: 0.8115 (mtp85) REVERT: D 272 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7742 (tp30) REVERT: D 318 GLU cc_start: 0.8305 (tt0) cc_final: 0.7946 (mt-10) outliers start: 49 outliers final: 8 residues processed: 201 average time/residue: 0.2437 time to fit residues: 72.0871 Evaluate side-chains 149 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 272 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 41 optimal weight: 0.0020 chunk 51 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 253 GLN B 119 GLN B 253 GLN C 119 GLN C 253 GLN D 119 GLN D 253 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.149077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115718 restraints weight = 17387.702| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.47 r_work: 0.3044 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13340 Z= 0.115 Angle : 0.674 9.377 18012 Z= 0.309 Chirality : 0.043 0.257 2096 Planarity : 0.005 0.041 2164 Dihedral : 19.476 166.371 2264 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.06 % Allowed : 15.67 % Favored : 81.27 % 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: -1.05 (0.22), residues: 1544 helix: 0.07 (0.18), residues: 908 sheet: -1.02 (0.52), residues: 92 loop : -1.85 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 264 HIS 0.002 0.001 HIS C 149 PHE 0.007 0.001 PHE D 242 TYR 0.010 0.001 TYR C 128 ARG 0.003 0.000 ARG D 399 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 560) hydrogen bonds : angle 3.71467 ( 1608) covalent geometry : bond 0.00261 (13340) covalent geometry : angle 0.67382 (18012) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 1.372 Fit side-chains REVERT: A 60 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7417 (tt) REVERT: A 126 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6842 (pp) REVERT: A 205 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8954 (mm) REVERT: A 230 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8668 (tp) REVERT: A 233 ARG cc_start: 0.8670 (ttt90) cc_final: 0.8293 (mtp85) REVERT: A 318 GLU cc_start: 0.8615 (tt0) cc_final: 0.8276 (mt-10) REVERT: B 60 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7399 (tt) REVERT: B 126 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6845 (pp) REVERT: B 205 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8947 (mm) REVERT: B 233 ARG cc_start: 0.8620 (ttt90) cc_final: 0.8259 (mtp85) REVERT: B 318 GLU cc_start: 0.8568 (tt0) cc_final: 0.8211 (mt-10) REVERT: C 60 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7408 (tt) REVERT: C 126 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6848 (pp) REVERT: C 171 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8498 (tp) REVERT: C 205 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8940 (mm) REVERT: C 230 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8639 (tp) REVERT: C 233 ARG cc_start: 0.8552 (ttt90) cc_final: 0.8229 (mtp85) REVERT: C 318 GLU cc_start: 0.8551 (tt0) cc_final: 0.8210 (mt-10) REVERT: D 60 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7471 (tt) REVERT: D 126 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6924 (pp) REVERT: D 171 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8535 (tp) REVERT: D 205 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8922 (mm) REVERT: D 230 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8649 (tp) REVERT: D 233 ARG cc_start: 0.8595 (ttt90) cc_final: 0.8266 (mtp85) REVERT: D 318 GLU cc_start: 0.8572 (tt0) cc_final: 0.8214 (mt-10) outliers start: 41 outliers final: 4 residues processed: 197 average time/residue: 0.2642 time to fit residues: 74.5065 Evaluate side-chains 153 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 230 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111165 restraints weight = 17337.187| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.63 r_work: 0.2947 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13340 Z= 0.183 Angle : 0.705 8.660 18012 Z= 0.327 Chirality : 0.046 0.257 2096 Planarity : 0.005 0.042 2164 Dihedral : 18.674 166.571 2264 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.55 % Allowed : 14.48 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1544 helix: 0.26 (0.18), residues: 916 sheet: -0.88 (0.50), residues: 84 loop : -1.60 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 264 HIS 0.002 0.001 HIS B 281 PHE 0.008 0.001 PHE D 366 TYR 0.013 0.001 TYR A 175 ARG 0.003 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03950 ( 560) hydrogen bonds : angle 3.70740 ( 1608) covalent geometry : bond 0.00446 (13340) covalent geometry : angle 0.70493 (18012) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 116 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7507 (tt) REVERT: A 114 LYS cc_start: 0.8107 (tptp) cc_final: 0.7772 (tttp) REVERT: A 126 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.6964 (pp) REVERT: A 205 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8718 (mm) REVERT: A 230 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8519 (tp) REVERT: A 233 ARG cc_start: 0.8514 (ttt90) cc_final: 0.8151 (mtp85) REVERT: A 272 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7819 (tp30) REVERT: A 318 GLU cc_start: 0.8450 (tt0) cc_final: 0.8124 (mt-10) REVERT: A 389 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8629 (pp) REVERT: B 60 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7365 (tt) REVERT: B 126 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6935 (pp) REVERT: B 233 ARG cc_start: 0.8478 (ttt90) cc_final: 0.8088 (mtp85) REVERT: B 272 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7818 (tp30) REVERT: B 318 GLU cc_start: 0.8432 (tt0) cc_final: 0.8094 (mt-10) REVERT: B 389 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8629 (pp) REVERT: C 60 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7377 (tt) REVERT: C 114 LYS cc_start: 0.8149 (tptp) cc_final: 0.7845 (tttp) REVERT: C 126 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7044 (pp) REVERT: C 230 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8512 (tp) REVERT: C 233 ARG cc_start: 0.8388 (ttt90) cc_final: 0.8091 (mtp85) REVERT: C 272 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7646 (tp30) REVERT: C 318 GLU cc_start: 0.8419 (tt0) cc_final: 0.8110 (mt-10) REVERT: D 60 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7502 (tt) REVERT: D 126 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7043 (pp) REVERT: D 205 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8709 (mm) REVERT: D 230 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8515 (tp) REVERT: D 233 ARG cc_start: 0.8426 (ttt90) cc_final: 0.8108 (mtp85) REVERT: D 272 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7650 (tp30) REVERT: D 318 GLU cc_start: 0.8430 (tt0) cc_final: 0.8106 (mt-10) outliers start: 61 outliers final: 27 residues processed: 174 average time/residue: 0.3111 time to fit residues: 77.0345 Evaluate side-chains 155 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 109 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 359 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 146 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 117 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.140321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106639 restraints weight = 17699.850| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.92 r_work: 0.2832 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13340 Z= 0.211 Angle : 0.706 8.434 18012 Z= 0.332 Chirality : 0.047 0.294 2096 Planarity : 0.005 0.043 2164 Dihedral : 18.403 166.400 2264 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.93 % Allowed : 15.15 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1544 helix: 0.19 (0.18), residues: 936 sheet: -1.07 (0.49), residues: 88 loop : -1.43 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 264 HIS 0.002 0.001 HIS B 232 PHE 0.007 0.001 PHE C 366 TYR 0.013 0.001 TYR A 175 ARG 0.003 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 560) hydrogen bonds : angle 3.75552 ( 1608) covalent geometry : bond 0.00521 (13340) covalent geometry : angle 0.70643 (18012) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 108 time to evaluate : 1.386 Fit side-chains REVERT: A 60 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7302 (tt) REVERT: A 114 LYS cc_start: 0.8102 (tptp) cc_final: 0.7711 (tttp) REVERT: A 126 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7137 (pp) REVERT: A 205 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8749 (mm) REVERT: A 230 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8488 (tp) REVERT: A 233 ARG cc_start: 0.8436 (ttt90) cc_final: 0.8054 (mtp85) REVERT: A 272 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7675 (tp30) REVERT: A 318 GLU cc_start: 0.8458 (tt0) cc_final: 0.8077 (mt-10) REVERT: B 60 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7328 (tt) REVERT: B 126 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7002 (pp) REVERT: B 205 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8725 (mm) REVERT: B 233 ARG cc_start: 0.8490 (ttt90) cc_final: 0.8091 (mtp85) REVERT: B 272 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7672 (tp30) REVERT: B 318 GLU cc_start: 0.8448 (tt0) cc_final: 0.8076 (mt-10) REVERT: C 60 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7315 (tt) REVERT: C 114 LYS cc_start: 0.8079 (tptp) cc_final: 0.7760 (tttp) REVERT: C 126 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7139 (pp) REVERT: C 205 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8734 (mm) REVERT: C 230 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8488 (tp) REVERT: C 233 ARG cc_start: 0.8370 (ttt90) cc_final: 0.8027 (mtp85) REVERT: C 272 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7656 (tp30) REVERT: C 318 GLU cc_start: 0.8471 (tt0) cc_final: 0.8079 (mt-10) REVERT: D 60 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7311 (tt) REVERT: D 114 LYS cc_start: 0.8043 (tptp) cc_final: 0.7667 (tttp) REVERT: D 126 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7140 (pp) REVERT: D 205 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8717 (mm) REVERT: D 230 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8485 (tp) REVERT: D 233 ARG cc_start: 0.8425 (ttt90) cc_final: 0.8080 (mtp85) REVERT: D 272 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.7662 (tp30) REVERT: D 318 GLU cc_start: 0.8440 (tt0) cc_final: 0.8073 (mt-10) outliers start: 66 outliers final: 27 residues processed: 172 average time/residue: 0.3091 time to fit residues: 76.1722 Evaluate side-chains 152 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 106 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 224 LYS Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 313 ILE Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 359 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 18 optimal weight: 0.8980 chunk 154 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 144 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.146284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.113526 restraints weight = 17639.270| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.70 r_work: 0.2832 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13340 Z= 0.124 Angle : 0.641 8.840 18012 Z= 0.296 Chirality : 0.043 0.273 2096 Planarity : 0.004 0.042 2164 Dihedral : 17.195 165.710 2264 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.66 % Allowed : 16.72 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.22), residues: 1544 helix: 0.62 (0.18), residues: 904 sheet: -0.70 (0.48), residues: 84 loop : -1.19 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 264 HIS 0.002 0.001 HIS B 232 PHE 0.006 0.001 PHE C 40 TYR 0.008 0.001 TYR A 175 ARG 0.002 0.000 ARG D 399 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 560) hydrogen bonds : angle 3.50934 ( 1608) covalent geometry : bond 0.00291 (13340) covalent geometry : angle 0.64098 (18012) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 120 time to evaluate : 1.352 Fit side-chains REVERT: A 60 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7250 (tt) REVERT: A 114 LYS cc_start: 0.8055 (tptp) cc_final: 0.7724 (tttp) REVERT: A 126 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.6959 (pp) REVERT: A 158 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8485 (pp) REVERT: A 205 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8689 (mm) REVERT: A 230 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8490 (tp) REVERT: A 233 ARG cc_start: 0.8357 (ttt90) cc_final: 0.7978 (mtp85) REVERT: A 272 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7725 (tp30) REVERT: A 318 GLU cc_start: 0.8435 (tt0) cc_final: 0.8028 (mt-10) REVERT: B 114 LYS cc_start: 0.7950 (tptp) cc_final: 0.7604 (tttp) REVERT: B 126 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6870 (pp) REVERT: B 158 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8485 (pp) REVERT: B 205 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8699 (mm) REVERT: B 233 ARG cc_start: 0.8392 (ttt90) cc_final: 0.7988 (mtp85) REVERT: B 272 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7727 (tp30) REVERT: B 318 GLU cc_start: 0.8430 (tt0) cc_final: 0.8032 (mt-10) REVERT: C 60 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7243 (tt) REVERT: C 114 LYS cc_start: 0.8037 (tptp) cc_final: 0.7715 (tttp) REVERT: C 126 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7041 (pp) REVERT: C 158 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8476 (pp) REVERT: C 205 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8704 (mm) REVERT: C 230 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8466 (tp) REVERT: C 233 ARG cc_start: 0.8262 (ttt90) cc_final: 0.7926 (mtp85) REVERT: C 272 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7687 (tp30) REVERT: C 318 GLU cc_start: 0.8434 (tt0) cc_final: 0.8015 (mt-10) REVERT: D 60 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7249 (tt) REVERT: D 114 LYS cc_start: 0.8009 (tptp) cc_final: 0.7667 (tttp) REVERT: D 126 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7077 (pp) REVERT: D 158 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8477 (pp) REVERT: D 205 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8691 (mm) REVERT: D 230 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8476 (tp) REVERT: D 233 ARG cc_start: 0.8326 (ttt90) cc_final: 0.7984 (mtp85) REVERT: D 272 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7707 (tp30) REVERT: D 318 GLU cc_start: 0.8446 (tt0) cc_final: 0.8008 (mt-10) outliers start: 49 outliers final: 19 residues processed: 169 average time/residue: 0.2734 time to fit residues: 65.6788 Evaluate side-chains 151 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 359 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 29 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 154 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.147339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114136 restraints weight = 17469.619| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.74 r_work: 0.2955 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13340 Z= 0.118 Angle : 0.628 8.915 18012 Z= 0.290 Chirality : 0.043 0.259 2096 Planarity : 0.004 0.042 2164 Dihedral : 16.414 165.352 2264 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.36 % Allowed : 17.24 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.23), residues: 1544 helix: 0.52 (0.18), residues: 952 sheet: -0.57 (0.49), residues: 92 loop : -1.43 (0.30), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 264 HIS 0.002 0.001 HIS B 232 PHE 0.006 0.001 PHE D 242 TYR 0.008 0.001 TYR A 175 ARG 0.005 0.000 ARG D 124 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 560) hydrogen bonds : angle 3.38899 ( 1608) covalent geometry : bond 0.00272 (13340) covalent geometry : angle 0.62816 (18012) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 1.342 Fit side-chains REVERT: A 114 LYS cc_start: 0.8044 (tptp) cc_final: 0.7707 (tttp) REVERT: A 126 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6931 (pp) REVERT: A 230 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8495 (tp) REVERT: A 233 ARG cc_start: 0.8325 (ttt90) cc_final: 0.7936 (mtp85) REVERT: A 272 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7761 (tp30) REVERT: A 318 GLU cc_start: 0.8439 (tt0) cc_final: 0.8035 (mt-10) REVERT: A 334 MET cc_start: 0.7555 (ttt) cc_final: 0.7108 (tpp) REVERT: B 47 ASP cc_start: 0.7095 (m-30) cc_final: 0.6884 (m-30) REVERT: B 114 LYS cc_start: 0.7939 (tptp) cc_final: 0.7570 (tttp) REVERT: B 126 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6792 (pp) REVERT: B 205 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8692 (mm) REVERT: B 233 ARG cc_start: 0.8408 (ttt90) cc_final: 0.7990 (mtp85) REVERT: B 272 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7764 (tp30) REVERT: B 318 GLU cc_start: 0.8439 (tt0) cc_final: 0.8038 (mt-10) REVERT: B 334 MET cc_start: 0.7495 (ttt) cc_final: 0.7065 (tpp) REVERT: C 114 LYS cc_start: 0.8086 (tptp) cc_final: 0.7734 (tttp) REVERT: C 126 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6895 (pp) REVERT: C 230 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8475 (tp) REVERT: C 233 ARG cc_start: 0.8280 (ttt90) cc_final: 0.7931 (mtp85) REVERT: C 272 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7731 (tp30) REVERT: C 318 GLU cc_start: 0.8445 (tt0) cc_final: 0.8055 (mt-10) REVERT: D 47 ASP cc_start: 0.7020 (m-30) cc_final: 0.6811 (m-30) REVERT: D 114 LYS cc_start: 0.8023 (tptp) cc_final: 0.7724 (tttp) REVERT: D 126 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6878 (pp) REVERT: D 230 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8475 (tp) REVERT: D 233 ARG cc_start: 0.8292 (ttt90) cc_final: 0.7935 (mtp85) REVERT: D 272 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7767 (tp30) REVERT: D 318 GLU cc_start: 0.8448 (tt0) cc_final: 0.8049 (mt-10) outliers start: 45 outliers final: 20 residues processed: 167 average time/residue: 0.2784 time to fit residues: 66.5428 Evaluate side-chains 153 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 359 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 143 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 118 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 137 optimal weight: 0.0980 chunk 124 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.114243 restraints weight = 17547.638| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.67 r_work: 0.3031 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13340 Z= 0.123 Angle : 0.629 10.561 18012 Z= 0.290 Chirality : 0.043 0.256 2096 Planarity : 0.004 0.039 2164 Dihedral : 16.248 165.145 2264 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.91 % Allowed : 17.01 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.23), residues: 1544 helix: 0.69 (0.18), residues: 952 sheet: -0.38 (0.51), residues: 92 loop : -1.27 (0.31), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 264 HIS 0.002 0.001 HIS C 149 PHE 0.006 0.001 PHE B 40 TYR 0.008 0.001 TYR B 175 ARG 0.002 0.000 ARG D 124 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 560) hydrogen bonds : angle 3.28152 ( 1608) covalent geometry : bond 0.00287 (13340) covalent geometry : angle 0.62903 (18012) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 1.368 Fit side-chains REVERT: A 114 LYS cc_start: 0.8090 (tptp) cc_final: 0.7750 (tttp) REVERT: A 126 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.6890 (pp) REVERT: A 230 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8533 (tp) REVERT: A 233 ARG cc_start: 0.8350 (ttt90) cc_final: 0.7970 (mtp85) REVERT: A 272 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7757 (tp30) REVERT: A 318 GLU cc_start: 0.8437 (tt0) cc_final: 0.8052 (mt-10) REVERT: A 334 MET cc_start: 0.7631 (ttt) cc_final: 0.7184 (tpp) REVERT: B 47 ASP cc_start: 0.7044 (m-30) cc_final: 0.6804 (m-30) REVERT: B 126 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6839 (pp) REVERT: B 205 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8709 (mm) REVERT: B 233 ARG cc_start: 0.8433 (ttt90) cc_final: 0.8001 (mtp85) REVERT: B 272 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7734 (tp30) REVERT: B 318 GLU cc_start: 0.8428 (tt0) cc_final: 0.8041 (mt-10) REVERT: B 334 MET cc_start: 0.7582 (ttt) cc_final: 0.7146 (tpp) REVERT: C 114 LYS cc_start: 0.8117 (tptp) cc_final: 0.7821 (tttp) REVERT: C 126 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6906 (pp) REVERT: C 230 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8509 (tp) REVERT: C 233 ARG cc_start: 0.8314 (ttt90) cc_final: 0.7954 (mtp85) REVERT: C 272 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7726 (tp30) REVERT: C 318 GLU cc_start: 0.8428 (tt0) cc_final: 0.8044 (mt-10) REVERT: D 47 ASP cc_start: 0.7024 (m-30) cc_final: 0.6785 (m-30) REVERT: D 126 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.6969 (pp) REVERT: D 230 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8517 (tp) REVERT: D 233 ARG cc_start: 0.8320 (ttt90) cc_final: 0.7958 (mtp85) REVERT: D 272 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7739 (tp30) REVERT: D 318 GLU cc_start: 0.8431 (tt0) cc_final: 0.8040 (mt-10) outliers start: 39 outliers final: 17 residues processed: 165 average time/residue: 0.2610 time to fit residues: 62.1998 Evaluate side-chains 151 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 359 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112476 restraints weight = 17567.668| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.78 r_work: 0.2979 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13340 Z= 0.123 Angle : 0.623 9.768 18012 Z= 0.287 Chirality : 0.043 0.260 2096 Planarity : 0.004 0.036 2164 Dihedral : 16.117 165.090 2264 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.46 % Allowed : 17.46 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 1544 helix: 0.81 (0.18), residues: 948 sheet: -0.35 (0.51), residues: 92 loop : -1.09 (0.31), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 264 HIS 0.002 0.001 HIS C 149 PHE 0.006 0.001 PHE C 40 TYR 0.008 0.001 TYR B 175 ARG 0.002 0.000 ARG D 124 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 560) hydrogen bonds : angle 3.24085 ( 1608) covalent geometry : bond 0.00286 (13340) covalent geometry : angle 0.62306 (18012) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 1.455 Fit side-chains REVERT: A 114 LYS cc_start: 0.8214 (tptp) cc_final: 0.7857 (tttp) REVERT: A 126 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6912 (pp) REVERT: A 230 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8557 (tp) REVERT: A 233 ARG cc_start: 0.8387 (ttt90) cc_final: 0.7999 (mtp85) REVERT: A 272 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7765 (tp30) REVERT: A 318 GLU cc_start: 0.8448 (tt0) cc_final: 0.8073 (mt-10) REVERT: A 334 MET cc_start: 0.7642 (ttt) cc_final: 0.7189 (tpp) REVERT: B 47 ASP cc_start: 0.7072 (m-30) cc_final: 0.6819 (m-30) REVERT: B 114 LYS cc_start: 0.8133 (tptt) cc_final: 0.7925 (tttp) REVERT: B 126 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6829 (pp) REVERT: B 205 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8749 (mm) REVERT: B 233 ARG cc_start: 0.8461 (ttt90) cc_final: 0.8019 (mtp85) REVERT: B 272 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7784 (tp30) REVERT: B 318 GLU cc_start: 0.8467 (tt0) cc_final: 0.8074 (mt-10) REVERT: B 334 MET cc_start: 0.7619 (ttt) cc_final: 0.7169 (tpp) REVERT: C 114 LYS cc_start: 0.8125 (tptp) cc_final: 0.7879 (tttp) REVERT: C 126 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6903 (pp) REVERT: C 230 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8537 (tp) REVERT: C 233 ARG cc_start: 0.8355 (ttt90) cc_final: 0.7985 (mtp85) REVERT: C 272 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7756 (tp30) REVERT: C 318 GLU cc_start: 0.8442 (tt0) cc_final: 0.8063 (mt-10) REVERT: C 334 MET cc_start: 0.7610 (ttt) cc_final: 0.7153 (tpp) REVERT: D 47 ASP cc_start: 0.7119 (m-30) cc_final: 0.6873 (m-30) REVERT: D 114 LYS cc_start: 0.8170 (tptt) cc_final: 0.7943 (tttp) REVERT: D 126 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6908 (pp) REVERT: D 230 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8545 (tp) REVERT: D 233 ARG cc_start: 0.8355 (ttt90) cc_final: 0.7980 (mtp85) REVERT: D 265 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8250 (tm-30) REVERT: D 272 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7731 (tp30) REVERT: D 318 GLU cc_start: 0.8436 (tt0) cc_final: 0.8059 (mt-10) REVERT: D 334 MET cc_start: 0.7643 (ttt) cc_final: 0.7186 (tpp) outliers start: 33 outliers final: 16 residues processed: 156 average time/residue: 0.2724 time to fit residues: 60.7954 Evaluate side-chains 150 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 401 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 42 optimal weight: 0.0570 chunk 24 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 120 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 5 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.139790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.102733 restraints weight = 17920.092| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.14 r_work: 0.2877 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13340 Z= 0.102 Angle : 0.606 9.208 18012 Z= 0.277 Chirality : 0.041 0.254 2096 Planarity : 0.004 0.036 2164 Dihedral : 15.753 164.552 2264 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.64 % Allowed : 18.58 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1544 helix: 0.86 (0.18), residues: 972 sheet: -0.28 (0.51), residues: 92 loop : -0.81 (0.31), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 264 HIS 0.002 0.001 HIS B 232 PHE 0.007 0.001 PHE B 40 TYR 0.007 0.001 TYR A 262 ARG 0.008 0.000 ARG D 124 Details of bonding type rmsd hydrogen bonds : bond 0.03000 ( 560) hydrogen bonds : angle 3.07170 ( 1608) covalent geometry : bond 0.00214 (13340) covalent geometry : angle 0.60583 (18012) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6826 (pp) REVERT: A 233 ARG cc_start: 0.8373 (ttt90) cc_final: 0.7987 (mtp85) REVERT: A 318 GLU cc_start: 0.8459 (tt0) cc_final: 0.8069 (mt-10) REVERT: A 334 MET cc_start: 0.7633 (ttt) cc_final: 0.7118 (tpp) REVERT: B 47 ASP cc_start: 0.7160 (m-30) cc_final: 0.6936 (m-30) REVERT: B 114 LYS cc_start: 0.8122 (tptt) cc_final: 0.7906 (tttp) REVERT: B 126 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6769 (pp) REVERT: B 233 ARG cc_start: 0.8458 (ttt90) cc_final: 0.8017 (mtp85) REVERT: B 318 GLU cc_start: 0.8483 (tt0) cc_final: 0.8070 (mt-10) REVERT: B 334 MET cc_start: 0.7600 (ttt) cc_final: 0.7087 (tpp) REVERT: C 114 LYS cc_start: 0.8087 (tptp) cc_final: 0.7857 (tttp) REVERT: C 126 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6853 (pp) REVERT: C 230 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8557 (tp) REVERT: C 233 ARG cc_start: 0.8351 (ttt90) cc_final: 0.7985 (mtp85) REVERT: C 318 GLU cc_start: 0.8451 (tt0) cc_final: 0.8047 (mt-10) REVERT: C 334 MET cc_start: 0.7671 (ttt) cc_final: 0.7193 (tpp) REVERT: D 114 LYS cc_start: 0.8191 (tptt) cc_final: 0.7934 (tttp) REVERT: D 126 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6737 (pp) REVERT: D 233 ARG cc_start: 0.8347 (ttt90) cc_final: 0.7974 (mtp85) REVERT: D 265 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8346 (tm-30) REVERT: D 272 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7774 (tp30) REVERT: D 318 GLU cc_start: 0.8441 (tt0) cc_final: 0.8061 (mt-10) REVERT: D 334 MET cc_start: 0.7617 (ttt) cc_final: 0.7103 (tpp) outliers start: 22 outliers final: 7 residues processed: 155 average time/residue: 0.2625 time to fit residues: 58.2629 Evaluate side-chains 128 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 130 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 117 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 127 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.102907 restraints weight = 18097.513| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.09 r_work: 0.2865 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13340 Z= 0.108 Angle : 0.604 9.090 18012 Z= 0.277 Chirality : 0.042 0.257 2096 Planarity : 0.004 0.037 2164 Dihedral : 15.621 164.692 2260 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.19 % Allowed : 19.33 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1544 helix: 1.09 (0.18), residues: 952 sheet: -0.18 (0.51), residues: 92 loop : -0.76 (0.33), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 264 HIS 0.002 0.001 HIS D 149 PHE 0.007 0.001 PHE B 40 TYR 0.006 0.001 TYR C 175 ARG 0.004 0.000 ARG D 124 Details of bonding type rmsd hydrogen bonds : bond 0.03129 ( 560) hydrogen bonds : angle 3.03790 ( 1608) covalent geometry : bond 0.00240 (13340) covalent geometry : angle 0.60426 (18012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5824.80 seconds wall clock time: 103 minutes 1.81 seconds (6181.81 seconds total)