Starting phenix.real_space_refine on Sat Oct 31 08:15:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rpd_54161/10_2026/9rpd_54161.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rpd_54161/10_2026/9rpd_54161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rpd_54161/10_2026/9rpd_54161.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rpd_54161/10_2026/9rpd_54161.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rpd_54161/10_2026/9rpd_54161.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rpd_54161/10_2026/9rpd_54161.map" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 S 146 5.16 5 C 13784 2.51 5 N 3724 2.21 5 O 4142 1.98 5 H 19714 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 295 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41510 Number of models: 1 Model: "" Number of chains: 5 Chain: "I" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 134 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain: "J" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1228 Classifications: {'peptide': 146} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 139} Chain breaks: 1 Chain: "K" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 104 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "B" Number of atoms: 6600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 6600 Classifications: {'peptide': 427} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Chain: "A" Number of atoms: 6711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6711 Classifications: {'peptide': 436} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 415} Restraints were copied for chains: C, E, G, D Time building chain proxies: 14.61, per 1000 atoms: 0.35 Number of scatterers: 41510 At special positions: 0 Unit cell: (117.59, 122.935, 164.626, 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 146 16.00 O 4142 8.00 N 3724 7.00 C 13784 6.00 H 19714 1.00 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 929.7 milliseconds 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5132 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 16 sheets defined 56.0% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'I' and resid 22 through 36 Processing helix chain 'J' and resid 11 through 31 removed outlier: 3.685A pdb=" N VAL J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 39 removed outlier: 3.510A pdb=" N LYS J 39 " --> pdb=" O ASP J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 66 Processing helix chain 'J' and resid 66 through 74 Processing helix chain 'J' and resid 80 through 102 Processing helix chain 'J' and resid 111 through 116 Processing helix chain 'J' and resid 119 through 145 Processing helix chain 'J' and resid 156 through 164 Processing helix chain 'K' and resid 64 through 75 Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.738A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 107 removed outlier: 3.513A pdb=" N THR B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 125 removed outlier: 5.118A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.609A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.525A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.563A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.587A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.916A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 41 through 46 removed outlier: 4.738A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 70 through 79 Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 100 through 107 removed outlier: 3.514A pdb=" N THR D 107 " --> pdb=" O LYS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 125 removed outlier: 5.118A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.610A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 221 through 237 removed outlier: 3.524A pdb=" N LEU D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 242 Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.562A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 299 Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 338 through 341 Processing helix chain 'D' and resid 374 through 390 removed outlier: 3.587A pdb=" N PHE D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET D 388 " --> pdb=" O GLN D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 404 through 427 removed outlier: 3.915A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.929A pdb=" N PHE A 49 " --> pdb=" O ASP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 109 through 127 removed outlier: 3.897A pdb=" N GLU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.217A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.534A pdb=" N SER A 178 " --> pdb=" O PRO A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.824A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.695A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 296 through 301 removed outlier: 6.724A pdb=" N ALA A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 339 Processing helix chain 'A' and resid 384 through 400 removed outlier: 3.881A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.146A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 436 removed outlier: 4.186A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 29 Processing helix chain 'C' and resid 46 through 51 removed outlier: 3.929A pdb=" N PHE C 49 " --> pdb=" O ASP C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 109 through 127 removed outlier: 3.898A pdb=" N GLU C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.216A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 178 removed outlier: 3.534A pdb=" N SER C 178 " --> pdb=" O PRO C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 223 through 244 removed outlier: 4.824A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.694A pdb=" N PHE C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 296 through 301 removed outlier: 6.723A pdb=" N ALA C 299 " --> pdb=" O PHE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 339 Processing helix chain 'C' and resid 384 through 400 removed outlier: 3.882A pdb=" N TRP C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.146A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 436 removed outlier: 4.185A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 29 Processing helix chain 'G' and resid 46 through 51 removed outlier: 3.930A pdb=" N PHE G 49 " --> pdb=" O ASP G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 81 Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 102 through 108 Processing helix chain 'G' and resid 109 through 127 removed outlier: 3.898A pdb=" N GLU G 113 " --> pdb=" O THR G 109 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE G 114 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N LEU G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 161 removed outlier: 4.216A pdb=" N THR G 150 " --> pdb=" O GLY G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 178 removed outlier: 3.534A pdb=" N SER G 178 " --> pdb=" O PRO G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 195 Processing helix chain 'G' and resid 206 through 217 Processing helix chain 'G' and resid 223 through 244 removed outlier: 4.824A pdb=" N SER G 241 " --> pdb=" O SER G 237 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU G 242 " --> pdb=" O ILE G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 260 removed outlier: 3.695A pdb=" N PHE G 255 " --> pdb=" O ASP G 251 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN G 256 " --> pdb=" O LEU G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 287 through 295 Processing helix chain 'G' and resid 296 through 301 removed outlier: 6.724A pdb=" N ALA G 299 " --> pdb=" O PHE G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 310 Processing helix chain 'G' and resid 324 through 339 Processing helix chain 'G' and resid 384 through 400 removed outlier: 3.882A pdb=" N TRP G 388 " --> pdb=" O ILE G 384 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS G 394 " --> pdb=" O ARG G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 410 removed outlier: 4.147A pdb=" N TYR G 408 " --> pdb=" O PHE G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 436 removed outlier: 4.186A pdb=" N PHE G 418 " --> pdb=" O GLU G 414 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER G 419 " --> pdb=" O GLU G 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 46 through 51 removed outlier: 3.930A pdb=" N PHE E 49 " --> pdb=" O ASP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 81 Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 109 through 127 removed outlier: 3.898A pdb=" N GLU E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.217A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.534A pdb=" N SER E 178 " --> pdb=" O PRO E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 206 through 217 Processing helix chain 'E' and resid 223 through 244 removed outlier: 4.824A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.695A pdb=" N PHE E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 281 Processing helix chain 'E' and resid 287 through 295 Processing helix chain 'E' and resid 296 through 301 removed outlier: 6.723A pdb=" N ALA E 299 " --> pdb=" O PHE E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 339 Processing helix chain 'E' and resid 384 through 400 removed outlier: 3.882A pdb=" N TRP E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS E 394 " --> pdb=" O ARG E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.147A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 436 removed outlier: 4.187A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.998A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.197A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.286A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA3, first strand: chain 'D' and resid 90 through 92 removed outlier: 7.999A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLU D 3 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY D 132 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER D 138 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ASN D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL D 169 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N HIS D 137 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE D 202 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER D 168 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 13.286A pdb=" N ASP D 203 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.117A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 273 removed outlier: 6.725A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.116A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB1, first strand: chain 'C' and resid 269 through 273 removed outlier: 6.725A pdb=" N ALA C 374 " --> pdb=" O TYR C 319 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR C 319 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS C 376 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 317 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU C 378 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N CYS C 315 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN C 380 " --> pdb=" O MET C 313 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 92 through 94 removed outlier: 8.117A pdb=" N ILE G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE G 67 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL G 66 " --> pdb=" O CYS G 4 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER G 6 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL G 68 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N HIS G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER G 140 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS G 166 " --> pdb=" O CYS G 200 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE G 202 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU G 168 " --> pdb=" O PHE G 202 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL G 204 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER G 170 " --> pdb=" O VAL G 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'G' and resid 269 through 273 removed outlier: 6.726A pdb=" N ALA G 374 " --> pdb=" O TYR G 319 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TYR G 319 " --> pdb=" O ALA G 374 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N CYS G 376 " --> pdb=" O LEU G 317 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU G 317 " --> pdb=" O CYS G 376 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU G 378 " --> pdb=" O CYS G 315 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N CYS G 315 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN G 380 " --> pdb=" O MET G 313 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.117A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER E 140 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB7, first strand: chain 'E' and resid 269 through 273 removed outlier: 6.725A pdb=" N ALA E 374 " --> pdb=" O TYR E 319 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR E 319 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N CYS E 376 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU E 317 " --> pdb=" O CYS E 376 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU E 378 " --> pdb=" O CYS E 315 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N CYS E 315 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN E 380 " --> pdb=" O MET E 313 " (cutoff:3.500A) 1125 hydrogen bonds defined for protein. 3213 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: 9.18 Time building geometry restraints manager: 5.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 19650 1.13 - 1.31: 4098 1.31 - 1.48: 8773 1.48 - 1.66: 9257 1.66 - 1.84: 228 Bond restraints: 42006 Sorted by residual: bond pdb=" C ALA J 107 " pdb=" N ASN J 108 " ideal model delta sigma weight residual 1.333 1.198 0.135 1.42e-02 4.96e+03 9.05e+01 bond pdb=" C LEU J 40 " pdb=" N ILE J 41 " ideal model delta sigma weight residual 1.331 1.236 0.096 1.11e-02 8.12e+03 7.41e+01 bond pdb=" C PHE J 54 " pdb=" N VAL J 55 " ideal model delta sigma weight residual 1.335 1.234 0.100 1.26e-02 6.30e+03 6.36e+01 bond pdb=" C ASP I 22 " pdb=" N ASP I 23 " ideal model delta sigma weight residual 1.332 1.224 0.108 1.40e-02 5.10e+03 5.98e+01 bond pdb=" C HIS J 31 " pdb=" N PRO J 32 " ideal model delta sigma weight residual 1.332 1.229 0.103 1.34e-02 5.57e+03 5.91e+01 ... (remaining 42001 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 67230 3.13 - 6.25: 6429 6.25 - 9.38: 1235 9.38 - 12.50: 66 12.50 - 15.63: 26 Bond angle restraints: 74986 Sorted by residual: angle pdb=" O MET J 116 " pdb=" C MET J 116 " pdb=" N PRO J 117 " ideal model delta sigma weight residual 121.34 129.60 -8.26 8.90e-01 1.26e+00 8.62e+01 angle pdb=" C LEU J 113 " pdb=" N VAL J 114 " pdb=" CA VAL J 114 " ideal model delta sigma weight residual 122.16 112.19 9.97 1.26e+00 6.30e-01 6.27e+01 angle pdb=" CA MET J 116 " pdb=" C MET J 116 " pdb=" N PRO J 117 " ideal model delta sigma weight residual 117.59 109.73 7.86 1.03e+00 9.43e-01 5.82e+01 angle pdb=" CA LEU J 113 " pdb=" C LEU J 113 " pdb=" N VAL J 114 " ideal model delta sigma weight residual 118.14 108.77 9.37 1.31e+00 5.83e-01 5.11e+01 angle pdb=" OE1 GLN D 131 " pdb=" CD GLN D 131 " pdb=" NE2 GLN D 131 " ideal model delta sigma weight residual 122.60 115.73 6.87 1.00e+00 1.00e+00 4.73e+01 ... (remaining 74981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.28: 18115 15.28 - 30.56: 1080 30.56 - 45.84: 408 45.84 - 61.12: 398 61.12 - 76.41: 138 Dihedral angle restraints: 20139 sinusoidal: 10740 harmonic: 9399 Sorted by residual: dihedral pdb=" CD2 HIS E 197 " pdb=" CG HIS E 197 " pdb=" ND1 HIS E 197 " pdb=" HD1 HIS E 197 " ideal model delta harmonic sigma weight residual 180.00 -156.53 -23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CD2 HIS A 197 " pdb=" CG HIS A 197 " pdb=" ND1 HIS A 197 " pdb=" HD1 HIS A 197 " ideal model delta harmonic sigma weight residual -180.00 -156.57 -23.43 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CD2 HIS C 197 " pdb=" CG HIS C 197 " pdb=" ND1 HIS C 197 " pdb=" HD1 HIS C 197 " ideal model delta harmonic sigma weight residual -180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 20136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2135 0.072 - 0.143: 938 0.143 - 0.214: 179 0.214 - 0.286: 51 0.286 - 0.357: 2 Chirality restraints: 3305 Sorted by residual: chirality pdb=" CA THR B 107 " pdb=" N THR B 107 " pdb=" C THR B 107 " pdb=" CB THR B 107 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA THR D 107 " pdb=" N THR D 107 " pdb=" C THR D 107 " pdb=" CB THR D 107 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CB THR D 33 " pdb=" CA THR D 33 " pdb=" OG1 THR D 33 " pdb=" CG2 THR D 33 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 3302 not shown) Planarity restraints: 6432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 2 " 0.623 9.50e-02 1.11e+02 2.79e-01 8.21e+02 pdb=" NE ARG D 2 " 0.239 2.00e-02 2.50e+03 pdb=" CZ ARG D 2 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG D 2 " -0.192 2.00e-02 2.50e+03 pdb=" NH2 ARG D 2 " 0.057 2.00e-02 2.50e+03 pdb="HH11 ARG D 2 " -0.163 2.00e-02 2.50e+03 pdb="HH12 ARG D 2 " 0.128 2.00e-02 2.50e+03 pdb="HH21 ARG D 2 " 0.229 2.00e-02 2.50e+03 pdb="HH22 ARG D 2 " -0.344 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 2 " -0.622 9.50e-02 1.11e+02 2.78e-01 8.19e+02 pdb=" NE ARG B 2 " -0.239 2.00e-02 2.50e+03 pdb=" CZ ARG B 2 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 2 " 0.192 2.00e-02 2.50e+03 pdb=" NH2 ARG B 2 " -0.057 2.00e-02 2.50e+03 pdb="HH11 ARG B 2 " 0.162 2.00e-02 2.50e+03 pdb="HH12 ARG B 2 " -0.128 2.00e-02 2.50e+03 pdb="HH21 ARG B 2 " -0.229 2.00e-02 2.50e+03 pdb="HH22 ARG B 2 " 0.343 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 165 " 0.188 2.00e-02 2.50e+03 1.97e-01 5.80e+02 pdb=" CG ASN B 165 " -0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN B 165 " -0.096 2.00e-02 2.50e+03 pdb=" ND2 ASN B 165 " -0.232 2.00e-02 2.50e+03 pdb="HD21 ASN B 165 " -0.128 2.00e-02 2.50e+03 pdb="HD22 ASN B 165 " 0.336 2.00e-02 2.50e+03 ... (remaining 6429 not shown) Histogram of nonbonded interaction distances: 0.17 - 1.05: 159 1.05 - 1.94: 1681 1.94 - 2.83: 85592 2.83 - 3.71: 188544 3.71 - 4.60: 318309 Warning: very small nonbonded interaction distances. Nonbonded interactions: 594285 Sorted by model distance: nonbonded pdb=" CG LYS D 324 " pdb=" HA ARG G 221 " model vdw 0.168 2.920 nonbonded pdb=" CG LYS B 324 " pdb=" HA ARG E 221 " model vdw 0.169 2.920 nonbonded pdb=" HE2 LYS B 324 " pdb=" O GLU E 220 " model vdw 0.341 2.620 nonbonded pdb=" HE2 LYS D 324 " pdb=" O GLU G 220 " model vdw 0.342 2.620 nonbonded pdb=" HB2 ASN B 247 " pdb=" OE2 GLU E 71 " model vdw 0.435 2.620 ... (remaining 594280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.100 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 44.210 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4587 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 : 0.016 0.381 22308 Z= 1.224 Angle : 1.618 10.387 30216 Z= 1.104 Chirality : 0.080 0.357 3305 Planarity : 0.014 0.157 3960 Dihedral : 11.461 76.406 8159 Min Nonbonded Distance : 0.818 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.76 % Favored : 97.17 % Rotamer: Outliers : 1.10 % Allowed : 0.72 % Favored : 98.17 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.14), residues: 2752 helix: -0.06 (0.13), residues: 1274 sheet: 0.06 (0.25), residues: 388 loop : -0.41 (0.17), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG D 213 TYR 0.094 0.013 TYR D 106 PHE 0.058 0.009 PHE G 141 TRP 0.064 0.020 TRP B 344 HIS 0.024 0.006 HIS G 139 Details of bonding type rmsd/Z covalent geometry : bond 0.01296 / 0.78 (22292) covalent geometry : angle 1.61782 / 1.10 (30216) hydrogen bonds : bond 0.17969 / 11.86 ( 1125) hydrogen bonds : angle 6.99722 / 4.94 ( 3213) Misc. bond : bond 0.35269 / 20.87 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 728 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 54 PHE cc_start: 0.8348 (t80) cc_final: 0.8030 (t80) REVERT: J 70 PHE cc_start: 0.7841 (t80) cc_final: 0.7454 (t80) REVERT: B 232 THR cc_start: 0.8247 (m) cc_final: 0.7957 (m) REVERT: B 266 PHE cc_start: 0.7706 (m-10) cc_final: 0.7466 (m-10) REVERT: D 73 MET cc_start: 0.8509 (mtp) cc_final: 0.8283 (mmm) REVERT: D 237 THR cc_start: 0.8266 (p) cc_final: 0.7892 (p) REVERT: D 266 PHE cc_start: 0.7651 (m-10) cc_final: 0.7028 (m-80) REVERT: A 20 CYS cc_start: 0.8185 (m) cc_final: 0.7042 (m) REVERT: A 73 THR cc_start: 0.7536 (m) cc_final: 0.7233 (p) REVERT: A 101 ASN cc_start: 0.5257 (m-40) cc_final: 0.4974 (p0) REVERT: A 149 PHE cc_start: 0.8215 (t80) cc_final: 0.7801 (t80) REVERT: C 149 PHE cc_start: 0.8100 (t80) cc_final: 0.7541 (t80) REVERT: C 167 LEU cc_start: 0.8766 (mp) cc_final: 0.8513 (tp) REVERT: C 328 VAL cc_start: 0.9157 (t) cc_final: 0.8723 (t) REVERT: G 167 LEU cc_start: 0.8902 (mp) cc_final: 0.8525 (mp) REVERT: E 150 THR cc_start: 0.8630 (m) cc_final: 0.8066 (p) REVERT: E 238 ILE cc_start: 0.7697 (mt) cc_final: 0.7306 (mt) REVERT: E 391 LEU cc_start: 0.9048 (tp) cc_final: 0.8833 (tp) outliers start: 26 outliers final: 8 residues processed: 747 average time/residue: 0.4197 time to fit residues: 451.5175 Evaluate side-chains 516 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 508 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 25 GLN J 16 GLN J 21 HIS J 56 HIS J 59 HIS J 102 HIS ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN A 50 ASN C 226 ASN ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN E 393 HIS ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.100092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.073535 restraints weight = 316119.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.078320 restraints weight = 206148.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.082177 restraints weight = 143230.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.085296 restraints weight = 104121.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.087737 restraints weight = 78218.529| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5626 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.178 22308 Z= 0.292 Angle : 0.786 28.642 30216 Z= 0.433 Chirality : 0.046 0.445 3305 Planarity : 0.007 0.120 3960 Dihedral : 5.246 28.061 3010 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.40 % Favored : 97.46 % Rotamer: Outliers : 0.34 % Allowed : 2.12 % Favored : 97.54 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.15), residues: 2752 helix: 1.20 (0.14), residues: 1276 sheet: -0.34 (0.24), residues: 404 loop : 0.06 (0.19), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 221 TYR 0.031 0.002 TYR E 210 PHE 0.015 0.002 PHE D 260 TRP 0.020 0.002 TRP B 344 HIS 0.014 0.002 HIS B 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.29 (22292) covalent geometry : angle 0.78553 / 0.43 (30216) hydrogen bonds : bond 0.06710 / 4.36 ( 1125) hydrogen bonds : angle 5.21936 / 3.74 ( 3213) Misc. bond : bond 0.01979 / 1.30 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 544 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 46 PHE cc_start: 0.8751 (m-80) cc_final: 0.7958 (m-80) REVERT: J 54 PHE cc_start: 0.9196 (t80) cc_final: 0.8902 (t80) REVERT: J 58 MET cc_start: 0.9656 (tpt) cc_final: 0.9238 (tpp) REVERT: J 70 PHE cc_start: 0.9108 (t80) cc_final: 0.8112 (t80) REVERT: J 94 TYR cc_start: 0.9188 (t80) cc_final: 0.8417 (t80) REVERT: J 142 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8351 (mm-30) REVERT: B 19 LYS cc_start: 0.9389 (mmtt) cc_final: 0.8917 (tttt) REVERT: B 137 HIS cc_start: 0.8945 (p-80) cc_final: 0.8655 (p-80) REVERT: B 292 GLN cc_start: 0.9234 (mt0) cc_final: 0.8987 (tt0) REVERT: B 330 MET cc_start: 0.8832 (mmm) cc_final: 0.8425 (mmm) REVERT: B 337 ASN cc_start: 0.9133 (m110) cc_final: 0.8923 (m-40) REVERT: B 341 PHE cc_start: 0.9119 (m-80) cc_final: 0.8795 (m-80) REVERT: D 266 PHE cc_start: 0.9419 (m-10) cc_final: 0.8959 (m-80) REVERT: D 322 SER cc_start: 0.8139 (OUTLIER) cc_final: 0.7637 (t) REVERT: D 389 PHE cc_start: 0.8287 (t80) cc_final: 0.8081 (t80) REVERT: D 408 PHE cc_start: 0.9649 (m-10) cc_final: 0.9399 (m-80) REVERT: D 412 GLU cc_start: 0.9392 (tm-30) cc_final: 0.8776 (tp30) REVERT: A 20 CYS cc_start: 0.9308 (m) cc_final: 0.8247 (p) REVERT: A 101 ASN cc_start: 0.6526 (m-40) cc_final: 0.5354 (t0) REVERT: A 202 PHE cc_start: 0.9073 (m-80) cc_final: 0.8287 (m-80) REVERT: A 234 ILE cc_start: 0.8465 (mp) cc_final: 0.8209 (mt) REVERT: C 168 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8422 (mp0) REVERT: C 202 PHE cc_start: 0.9363 (m-80) cc_final: 0.8989 (m-80) REVERT: C 319 TYR cc_start: 0.9359 (m-10) cc_final: 0.9044 (m-80) REVERT: G 157 LEU cc_start: 0.9137 (mt) cc_final: 0.8851 (mt) REVERT: G 169 PHE cc_start: 0.9284 (m-80) cc_final: 0.8885 (m-80) REVERT: G 199 ASP cc_start: 0.9569 (m-30) cc_final: 0.8899 (t0) REVERT: G 292 THR cc_start: 0.8783 (p) cc_final: 0.8573 (p) REVERT: E 138 PHE cc_start: 0.8664 (m-80) cc_final: 0.8311 (m-80) outliers start: 8 outliers final: 4 residues processed: 552 average time/residue: 0.4093 time to fit residues: 328.9258 Evaluate side-chains 453 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 448 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: [176, 251, 95, 223, 267, 14, 185, 162, 253, 102, 134] chunk 176 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 223 optimal weight: 20.0000 chunk 267 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 185 optimal weight: 30.0000 chunk 162 optimal weight: 20.0000 chunk 253 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 414 ASN ** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN D 423 GLN C 91 GLN ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.093914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.068526 restraints weight = 321357.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.073046 restraints weight = 207643.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.076667 restraints weight = 144067.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.079569 restraints weight = 104836.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.081855 restraints weight = 78963.883| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.207 22308 Z= 0.267 Angle : 0.762 31.246 30216 Z= 0.417 Chirality : 0.043 0.244 3305 Planarity : 0.008 0.216 3960 Dihedral : 5.260 39.650 3010 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.66 % Rotamer: Outliers : 0.08 % Allowed : 1.91 % Favored : 98.00 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.15), residues: 2752 helix: 0.88 (0.13), residues: 1286 sheet: -0.30 (0.24), residues: 388 loop : -0.23 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 221 TYR 0.030 0.002 TYR E 210 PHE 0.028 0.002 PHE C 351 TRP 0.024 0.002 TRP C 346 HIS 0.024 0.002 HIS G 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.26 (22292) covalent geometry : angle 0.76176 / 0.42 (30216) hydrogen bonds : bond 0.06207 / 3.98 ( 1125) hydrogen bonds : angle 5.08972 / 3.67 ( 3213) Misc. bond : bond 0.01897 / 1.33 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 485 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 46 PHE cc_start: 0.8677 (m-80) cc_final: 0.7681 (m-80) REVERT: J 54 PHE cc_start: 0.9174 (t80) cc_final: 0.8875 (t80) REVERT: J 65 LEU cc_start: 0.8426 (tp) cc_final: 0.8127 (tt) REVERT: J 70 PHE cc_start: 0.9139 (t80) cc_final: 0.8023 (t80) REVERT: J 73 ARG cc_start: 0.8583 (tpm170) cc_final: 0.8361 (tpm170) REVERT: J 94 TYR cc_start: 0.9282 (t80) cc_final: 0.8631 (t80) REVERT: J 116 MET cc_start: 0.9244 (tmm) cc_final: 0.9023 (tmm) REVERT: J 137 LEU cc_start: 0.9682 (mt) cc_final: 0.9314 (mt) REVERT: J 142 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8340 (mm-30) REVERT: B 330 MET cc_start: 0.9055 (mmm) cc_final: 0.8664 (mmm) REVERT: D 66 VAL cc_start: 0.8902 (t) cc_final: 0.8548 (m) REVERT: D 266 PHE cc_start: 0.9250 (m-10) cc_final: 0.8996 (m-80) REVERT: D 408 PHE cc_start: 0.9704 (m-10) cc_final: 0.9490 (m-80) REVERT: A 101 ASN cc_start: 0.6598 (m-40) cc_final: 0.5175 (t0) REVERT: A 169 PHE cc_start: 0.8763 (m-80) cc_final: 0.8173 (m-80) REVERT: A 202 PHE cc_start: 0.8803 (m-80) cc_final: 0.8378 (m-80) REVERT: A 255 PHE cc_start: 0.9305 (m-80) cc_final: 0.8922 (m-80) REVERT: A 296 PHE cc_start: 0.9292 (m-80) cc_final: 0.8966 (m-80) REVERT: A 417 GLU cc_start: 0.9383 (mt-10) cc_final: 0.9022 (tp30) REVERT: A 425 MET cc_start: 0.9221 (mmp) cc_final: 0.8835 (mmm) REVERT: C 168 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8460 (mp0) REVERT: C 169 PHE cc_start: 0.9025 (m-10) cc_final: 0.8588 (m-80) REVERT: C 253 THR cc_start: 0.9179 (m) cc_final: 0.8916 (p) REVERT: C 255 PHE cc_start: 0.8902 (m-80) cc_final: 0.8329 (m-80) REVERT: C 292 THR cc_start: 0.9373 (p) cc_final: 0.9040 (p) REVERT: C 319 TYR cc_start: 0.9391 (m-10) cc_final: 0.9086 (m-80) REVERT: C 339 ARG cc_start: 0.3990 (mpt90) cc_final: 0.3462 (mpt180) REVERT: G 157 LEU cc_start: 0.9192 (mt) cc_final: 0.8867 (mt) REVERT: G 169 PHE cc_start: 0.9362 (m-80) cc_final: 0.8738 (m-80) REVERT: G 199 ASP cc_start: 0.9589 (m-30) cc_final: 0.9061 (t0) REVERT: G 313 MET cc_start: 0.5989 (mmp) cc_final: 0.4687 (mmp) REVERT: G 319 TYR cc_start: 0.9426 (m-10) cc_final: 0.9106 (m-80) REVERT: E 255 PHE cc_start: 0.8709 (m-80) cc_final: 0.8091 (m-80) REVERT: E 296 PHE cc_start: 0.9200 (m-80) cc_final: 0.8902 (t80) REVERT: E 398 MET cc_start: 0.9263 (mtm) cc_final: 0.8840 (mtp) outliers start: 2 outliers final: 2 residues processed: 487 average time/residue: 0.4028 time to fit residues: 287.2872 Evaluate side-chains 408 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 406 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: [220, 41, 52, 203, 137, 181, 104, 14, 190, 259, 182] chunk 220 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 52 optimal weight: 30.0000 chunk 203 optimal weight: 10.0000 chunk 137 optimal weight: 40.0000 chunk 181 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 259 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 25 GLN ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 ASN ** G 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN E 406 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.092542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.066819 restraints weight = 313953.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.071271 restraints weight = 202864.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.074897 restraints weight = 140822.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.077789 restraints weight = 102447.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.080153 restraints weight = 77421.127| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5982 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 22308 Z= 0.229 Angle : 0.663 21.049 30216 Z= 0.368 Chirality : 0.042 0.217 3305 Planarity : 0.007 0.232 3960 Dihedral : 5.120 40.487 3010 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.27 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 2752 helix: 0.86 (0.14), residues: 1287 sheet: -0.90 (0.24), residues: 398 loop : -0.18 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 221 TYR 0.025 0.002 TYR E 210 PHE 0.029 0.002 PHE E 138 TRP 0.018 0.002 TRP B 397 HIS 0.018 0.002 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.22 (22292) covalent geometry : angle 0.66313 / 0.37 (30216) hydrogen bonds : bond 0.05599 / 3.57 ( 1125) hydrogen bonds : angle 5.03889 / 3.64 ( 3213) Misc. bond : bond 0.01590 / 1.01 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 MET cc_start: 0.9683 (tpt) cc_final: 0.9438 (tpp) REVERT: J 65 LEU cc_start: 0.8154 (tp) cc_final: 0.7631 (tt) REVERT: J 70 PHE cc_start: 0.9035 (t80) cc_final: 0.8011 (t80) REVERT: J 74 PHE cc_start: 0.7867 (m-10) cc_final: 0.7141 (m-10) REVERT: J 94 TYR cc_start: 0.9303 (t80) cc_final: 0.8667 (t80) REVERT: J 137 LEU cc_start: 0.9604 (mt) cc_final: 0.9346 (mt) REVERT: J 142 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8486 (mm-30) REVERT: B 198 GLU cc_start: 0.9655 (mt-10) cc_final: 0.9278 (mt-10) REVERT: D 68 LEU cc_start: 0.9171 (mm) cc_final: 0.8788 (mm) REVERT: D 111 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8274 (mt-10) REVERT: D 128 ASP cc_start: 0.8037 (m-30) cc_final: 0.7770 (m-30) REVERT: A 1 MET cc_start: 0.8146 (tmm) cc_final: 0.7875 (tpt) REVERT: A 169 PHE cc_start: 0.8889 (m-80) cc_final: 0.8195 (m-80) REVERT: A 202 PHE cc_start: 0.8629 (m-80) cc_final: 0.8119 (m-80) REVERT: A 238 ILE cc_start: 0.9030 (mt) cc_final: 0.8811 (mt) REVERT: A 255 PHE cc_start: 0.9360 (m-80) cc_final: 0.8998 (m-80) REVERT: A 296 PHE cc_start: 0.9338 (m-80) cc_final: 0.9058 (m-10) REVERT: A 386 GLU cc_start: 0.9162 (mp0) cc_final: 0.8823 (mp0) REVERT: A 417 GLU cc_start: 0.9368 (mt-10) cc_final: 0.9031 (tp30) REVERT: A 425 MET cc_start: 0.9196 (mmp) cc_final: 0.8756 (mmm) REVERT: C 169 PHE cc_start: 0.8882 (m-10) cc_final: 0.8332 (m-80) REVERT: C 202 PHE cc_start: 0.9225 (m-80) cc_final: 0.8861 (m-80) REVERT: C 253 THR cc_start: 0.9084 (m) cc_final: 0.8869 (p) REVERT: C 255 PHE cc_start: 0.9065 (m-80) cc_final: 0.8467 (m-80) REVERT: C 334 THR cc_start: 0.7614 (p) cc_final: 0.7238 (p) REVERT: G 137 VAL cc_start: 0.9303 (t) cc_final: 0.9050 (p) REVERT: G 154 MET cc_start: 0.9374 (mmm) cc_final: 0.8997 (mmm) REVERT: G 169 PHE cc_start: 0.9331 (m-80) cc_final: 0.8627 (m-80) REVERT: G 199 ASP cc_start: 0.9636 (m-30) cc_final: 0.8909 (t0) REVERT: G 319 TYR cc_start: 0.9363 (m-10) cc_final: 0.9040 (m-80) REVERT: E 255 PHE cc_start: 0.8760 (m-80) cc_final: 0.8192 (m-80) REVERT: E 398 MET cc_start: 0.9197 (mtm) cc_final: 0.8820 (mtp) outliers start: 0 outliers final: 0 residues processed: 473 average time/residue: 0.4129 time to fit residues: 284.5568 Evaluate side-chains 405 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: [57, 1, 56, 60, 48, 130, 113, 182, 213, 172, 47] chunk 57 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 113 optimal weight: 20.0000 chunk 182 optimal weight: 20.0000 chunk 213 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN G 406 HIS ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.089923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.065869 restraints weight = 335837.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.070195 restraints weight = 215184.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.073680 restraints weight = 148129.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.076466 restraints weight = 106930.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.078646 restraints weight = 80082.637| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.6697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 22308 Z= 0.241 Angle : 0.668 21.939 30216 Z= 0.373 Chirality : 0.042 0.226 3305 Planarity : 0.007 0.228 3960 Dihedral : 5.090 35.247 3010 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.97 % Rotamer: Outliers : 0.04 % Allowed : 0.89 % Favored : 99.07 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.16), residues: 2752 helix: 0.87 (0.14), residues: 1255 sheet: -0.94 (0.24), residues: 398 loop : -0.22 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 2 TYR 0.028 0.002 TYR E 210 PHE 0.030 0.002 PHE A 169 TRP 0.013 0.002 TRP C 346 HIS 0.019 0.002 HIS E 8 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.24 (22292) covalent geometry : angle 0.66811 / 0.37 (30216) hydrogen bonds : bond 0.05532 / 3.54 ( 1125) hydrogen bonds : angle 5.06888 / 3.65 ( 3213) Misc. bond : bond 0.01683 / 1.07 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 466 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 MET cc_start: 0.9759 (tpt) cc_final: 0.9449 (tpp) REVERT: J 65 LEU cc_start: 0.8177 (tp) cc_final: 0.7775 (tt) REVERT: J 70 PHE cc_start: 0.9059 (t80) cc_final: 0.8054 (t80) REVERT: J 74 PHE cc_start: 0.8178 (m-10) cc_final: 0.7396 (m-10) REVERT: J 94 TYR cc_start: 0.9346 (t80) cc_final: 0.8799 (t80) REVERT: J 98 LEU cc_start: 0.9809 (mt) cc_final: 0.9494 (mt) REVERT: J 159 MET cc_start: 0.8331 (mpp) cc_final: 0.7758 (mpp) REVERT: B 67 ASP cc_start: 0.6485 (t0) cc_final: 0.5618 (p0) REVERT: B 198 GLU cc_start: 0.9683 (mt-10) cc_final: 0.9363 (mt-10) REVERT: B 318 ARG cc_start: 0.8498 (mtp180) cc_final: 0.7755 (mmm-85) REVERT: B 331 LEU cc_start: 0.9688 (mt) cc_final: 0.9463 (mt) REVERT: D 408 PHE cc_start: 0.9579 (m-80) cc_final: 0.9343 (m-80) REVERT: A 139 HIS cc_start: 0.8635 (p-80) cc_final: 0.7855 (p90) REVERT: A 169 PHE cc_start: 0.8852 (m-80) cc_final: 0.8625 (m-80) REVERT: A 202 PHE cc_start: 0.8762 (m-80) cc_final: 0.8317 (m-80) REVERT: A 203 MET cc_start: 0.6658 (mtm) cc_final: 0.6094 (mtm) REVERT: A 255 PHE cc_start: 0.9374 (m-80) cc_final: 0.8995 (m-80) REVERT: A 296 PHE cc_start: 0.9426 (m-80) cc_final: 0.9072 (m-80) REVERT: A 417 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9133 (tp30) REVERT: A 425 MET cc_start: 0.9180 (mmp) cc_final: 0.8801 (mmm) REVERT: C 253 THR cc_start: 0.9260 (m) cc_final: 0.8933 (p) REVERT: C 255 PHE cc_start: 0.9128 (m-80) cc_final: 0.8573 (m-80) REVERT: C 313 MET cc_start: 0.4857 (mmp) cc_final: 0.3191 (mmp) REVERT: C 339 ARG cc_start: 0.1506 (mpt180) cc_final: 0.1194 (mpt180) REVERT: G 137 VAL cc_start: 0.9322 (t) cc_final: 0.9071 (p) REVERT: G 154 MET cc_start: 0.9410 (mmm) cc_final: 0.9046 (mmm) REVERT: G 169 PHE cc_start: 0.9365 (m-80) cc_final: 0.8688 (m-80) REVERT: G 199 ASP cc_start: 0.9582 (m-30) cc_final: 0.8986 (t0) REVERT: G 319 TYR cc_start: 0.9388 (m-10) cc_final: 0.9080 (m-80) REVERT: E 255 PHE cc_start: 0.8726 (m-80) cc_final: 0.8095 (m-80) REVERT: E 398 MET cc_start: 0.9180 (mtm) cc_final: 0.8736 (mtp) outliers start: 1 outliers final: 1 residues processed: 466 average time/residue: 0.3971 time to fit residues: 272.7440 Evaluate side-chains 399 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 398 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: [2, 228, 53, 120, 59, 78, 213, 21, 14, 164, 271] chunk 2 optimal weight: 10.0000 chunk 228 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 213 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 164 optimal weight: 10.0000 chunk 271 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.087492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.065136 restraints weight = 349326.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.069191 restraints weight = 223879.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.072433 restraints weight = 154348.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.074951 restraints weight = 111802.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.076919 restraints weight = 84277.053| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 22308 Z= 0.255 Angle : 0.694 17.772 30216 Z= 0.393 Chirality : 0.042 0.257 3305 Planarity : 0.008 0.257 3960 Dihedral : 5.385 47.721 3010 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.32 % Favored : 95.60 % Rotamer: Outliers : 0.08 % Allowed : 0.93 % Favored : 98.98 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 2752 helix: 0.44 (0.14), residues: 1265 sheet: -0.69 (0.25), residues: 368 loop : -0.61 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG G 221 TYR 0.025 0.002 TYR E 210 PHE 0.025 0.002 PHE D 167 TRP 0.018 0.002 TRP B 344 HIS 0.012 0.002 HIS G 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.25 (22292) covalent geometry : angle 0.69407 / 0.39 (30216) hydrogen bonds : bond 0.05546 / 3.56 ( 1125) hydrogen bonds : angle 5.26323 / 3.80 ( 3213) Misc. bond : bond 0.01492 / 1.00 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 454 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 MET cc_start: 0.9814 (tpt) cc_final: 0.9425 (tpp) REVERT: J 65 LEU cc_start: 0.8310 (tp) cc_final: 0.7838 (tt) REVERT: J 70 PHE cc_start: 0.9117 (t80) cc_final: 0.8233 (t80) REVERT: J 74 PHE cc_start: 0.8640 (m-10) cc_final: 0.7940 (m-10) REVERT: J 94 TYR cc_start: 0.9369 (t80) cc_final: 0.8668 (t80) REVERT: J 116 MET cc_start: 0.9061 (tmm) cc_final: 0.8779 (tmm) REVERT: B 67 ASP cc_start: 0.6780 (t0) cc_final: 0.5434 (p0) REVERT: B 137 HIS cc_start: 0.9352 (p90) cc_final: 0.9122 (p-80) REVERT: B 198 GLU cc_start: 0.9731 (mt-10) cc_final: 0.9524 (mt-10) REVERT: B 201 CYS cc_start: 0.7923 (m) cc_final: 0.7643 (p) REVERT: B 330 MET cc_start: 0.9069 (ttp) cc_final: 0.8442 (mmm) REVERT: D 128 ASP cc_start: 0.8057 (m-30) cc_final: 0.7848 (m-30) REVERT: A 169 PHE cc_start: 0.9034 (m-80) cc_final: 0.8772 (m-80) REVERT: A 255 PHE cc_start: 0.9373 (m-80) cc_final: 0.9001 (m-80) REVERT: A 267 PHE cc_start: 0.8875 (m-80) cc_final: 0.8552 (m-80) REVERT: A 386 GLU cc_start: 0.9179 (mp0) cc_final: 0.8761 (mp0) REVERT: A 417 GLU cc_start: 0.9287 (mt-10) cc_final: 0.9083 (tp30) REVERT: A 425 MET cc_start: 0.9293 (mmp) cc_final: 0.8854 (mmm) REVERT: C 253 THR cc_start: 0.9293 (m) cc_final: 0.9018 (p) REVERT: C 313 MET cc_start: 0.5438 (mmp) cc_final: 0.3880 (mmp) REVERT: G 137 VAL cc_start: 0.9339 (t) cc_final: 0.9074 (p) REVERT: G 157 LEU cc_start: 0.9231 (mt) cc_final: 0.8971 (mt) REVERT: G 169 PHE cc_start: 0.9452 (m-80) cc_final: 0.8816 (m-80) REVERT: G 199 ASP cc_start: 0.9580 (m-30) cc_final: 0.9063 (t0) REVERT: G 313 MET cc_start: 0.6343 (mmp) cc_final: 0.5015 (mmp) REVERT: G 319 TYR cc_start: 0.9451 (m-10) cc_final: 0.9116 (m-80) REVERT: E 255 PHE cc_start: 0.8733 (m-80) cc_final: 0.8197 (m-80) REVERT: E 398 MET cc_start: 0.9069 (mtm) cc_final: 0.8595 (mtp) outliers start: 2 outliers final: 2 residues processed: 455 average time/residue: 0.3985 time to fit residues: 266.3607 Evaluate side-chains 397 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 395 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: [137, 203, 253, 128, 49, 38, 178, 117, 261, 62, 177] chunk 137 optimal weight: 20.0000 chunk 203 optimal weight: 9.9990 chunk 253 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN ** A 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.087688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.065224 restraints weight = 346749.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.069327 restraints weight = 221059.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.072613 restraints weight = 151570.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.075169 restraints weight = 109169.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.077193 restraints weight = 81867.212| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.7665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 22308 Z= 0.201 Angle : 0.623 19.978 30216 Z= 0.349 Chirality : 0.042 0.260 3305 Planarity : 0.007 0.221 3960 Dihedral : 5.161 48.445 3010 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.51 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.16), residues: 2752 helix: 0.83 (0.14), residues: 1257 sheet: -0.67 (0.25), residues: 364 loop : -0.55 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG G 221 TYR 0.026 0.002 TYR E 210 PHE 0.020 0.002 PHE C 351 TRP 0.015 0.002 TRP B 344 HIS 0.012 0.002 HIS G 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.20 (22292) covalent geometry : angle 0.62256 / 0.35 (30216) hydrogen bonds : bond 0.05248 / 3.33 ( 1125) hydrogen bonds : angle 5.10552 / 3.67 ( 3213) Misc. bond : bond 0.01611 / 1.05 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 MET cc_start: 0.9806 (tpt) cc_final: 0.9378 (tpp) REVERT: J 65 LEU cc_start: 0.8307 (tp) cc_final: 0.7741 (tt) REVERT: J 70 PHE cc_start: 0.9013 (t80) cc_final: 0.8114 (t80) REVERT: J 74 PHE cc_start: 0.8706 (m-10) cc_final: 0.7919 (m-10) REVERT: J 94 TYR cc_start: 0.9331 (t80) cc_final: 0.8707 (t80) REVERT: B 67 ASP cc_start: 0.6751 (t0) cc_final: 0.5647 (p0) REVERT: B 201 CYS cc_start: 0.8004 (m) cc_final: 0.7755 (p) REVERT: B 298 ASN cc_start: 0.9531 (m110) cc_final: 0.9188 (t0) REVERT: B 330 MET cc_start: 0.8959 (ttp) cc_final: 0.8471 (mmm) REVERT: B 345 ILE cc_start: 0.7890 (mm) cc_final: 0.7680 (mm) REVERT: D 165 ASN cc_start: 0.9567 (t0) cc_final: 0.9292 (t0) REVERT: D 265 PHE cc_start: 0.9356 (m-80) cc_final: 0.9063 (m-80) REVERT: D 266 PHE cc_start: 0.9041 (m-10) cc_final: 0.8723 (m-80) REVERT: D 293 MET cc_start: 0.9416 (ttp) cc_final: 0.9191 (tmm) REVERT: A 169 PHE cc_start: 0.9076 (m-80) cc_final: 0.8655 (m-80) REVERT: A 202 PHE cc_start: 0.8786 (m-80) cc_final: 0.8385 (m-80) REVERT: A 255 PHE cc_start: 0.9352 (m-80) cc_final: 0.8953 (m-80) REVERT: A 267 PHE cc_start: 0.8776 (m-80) cc_final: 0.8427 (m-80) REVERT: A 386 GLU cc_start: 0.9272 (mp0) cc_final: 0.8859 (mp0) REVERT: A 417 GLU cc_start: 0.9330 (mt-10) cc_final: 0.9111 (tp30) REVERT: A 425 MET cc_start: 0.9236 (mmp) cc_final: 0.8790 (mmm) REVERT: C 77 GLU cc_start: 0.9155 (mp0) cc_final: 0.8928 (mp0) REVERT: C 172 TYR cc_start: 0.3676 (t80) cc_final: 0.3324 (t80) REVERT: C 253 THR cc_start: 0.9310 (m) cc_final: 0.9034 (p) REVERT: C 313 MET cc_start: 0.5662 (mmp) cc_final: 0.3818 (mmp) REVERT: G 73 THR cc_start: 0.8658 (m) cc_final: 0.8351 (m) REVERT: G 77 GLU cc_start: 0.9294 (mm-30) cc_final: 0.9050 (mm-30) REVERT: G 137 VAL cc_start: 0.9334 (t) cc_final: 0.9056 (p) REVERT: G 157 LEU cc_start: 0.9229 (mt) cc_final: 0.8976 (mt) REVERT: G 169 PHE cc_start: 0.9422 (m-80) cc_final: 0.8768 (m-80) REVERT: G 199 ASP cc_start: 0.9570 (m-30) cc_final: 0.9029 (t0) REVERT: G 313 MET cc_start: 0.6331 (mmp) cc_final: 0.4991 (mmp) REVERT: G 319 TYR cc_start: 0.9421 (m-10) cc_final: 0.9114 (m-80) REVERT: E 255 PHE cc_start: 0.8739 (m-80) cc_final: 0.8169 (m-80) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.3877 time to fit residues: 257.1727 Evaluate side-chains 393 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: [13, 184, 42, 174, 133, 74, 7, 123, 190, 138, 81] chunk 13 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 190 optimal weight: 40.0000 chunk 138 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 ASN ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.085657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.063808 restraints weight = 353358.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.067844 restraints weight = 223945.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.071010 restraints weight = 152993.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.073515 restraints weight = 110001.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.075458 restraints weight = 82462.251| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.8152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 22308 Z= 0.210 Angle : 0.633 20.507 30216 Z= 0.356 Chirality : 0.042 0.255 3305 Planarity : 0.007 0.222 3960 Dihedral : 5.158 54.315 3010 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.16), residues: 2752 helix: 0.82 (0.14), residues: 1257 sheet: -0.74 (0.26), residues: 360 loop : -0.59 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 221 TYR 0.024 0.002 TYR G 224 PHE 0.023 0.002 PHE C 351 TRP 0.015 0.002 TRP B 344 HIS 0.010 0.002 HIS G 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.21 (22292) covalent geometry : angle 0.63329 / 0.36 (30216) hydrogen bonds : bond 0.05255 / 3.33 ( 1125) hydrogen bonds : angle 5.05994 / 3.63 ( 3213) Misc. bond : bond 0.01394 / 0.90 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 MET cc_start: 0.9803 (tpt) cc_final: 0.9351 (tpp) REVERT: J 65 LEU cc_start: 0.8556 (tp) cc_final: 0.7993 (tt) REVERT: J 70 PHE cc_start: 0.8908 (t80) cc_final: 0.8001 (t80) REVERT: J 74 PHE cc_start: 0.8863 (m-10) cc_final: 0.8108 (m-10) REVERT: J 94 TYR cc_start: 0.9314 (t80) cc_final: 0.8711 (t80) REVERT: J 129 PHE cc_start: 0.9603 (t80) cc_final: 0.9398 (t80) REVERT: B 167 PHE cc_start: 0.9029 (m-10) cc_final: 0.8506 (m-80) REVERT: B 198 GLU cc_start: 0.9752 (mt-10) cc_final: 0.9521 (mp0) REVERT: B 200 TYR cc_start: 0.9059 (m-80) cc_final: 0.8825 (m-80) REVERT: B 267 MET cc_start: 0.7420 (mtt) cc_final: 0.7204 (mtt) REVERT: B 298 ASN cc_start: 0.9533 (m110) cc_final: 0.9125 (t0) REVERT: B 330 MET cc_start: 0.9029 (ttp) cc_final: 0.8470 (mmm) REVERT: D 128 ASP cc_start: 0.8146 (m-30) cc_final: 0.7938 (m-30) REVERT: D 265 PHE cc_start: 0.9453 (m-80) cc_final: 0.9042 (m-80) REVERT: D 293 MET cc_start: 0.9392 (ttp) cc_final: 0.9171 (tmm) REVERT: D 408 PHE cc_start: 0.9506 (m-80) cc_final: 0.9288 (m-80) REVERT: A 169 PHE cc_start: 0.9141 (m-80) cc_final: 0.8857 (m-80) REVERT: A 202 PHE cc_start: 0.8699 (m-80) cc_final: 0.8416 (m-80) REVERT: A 255 PHE cc_start: 0.9381 (m-80) cc_final: 0.9006 (m-80) REVERT: A 267 PHE cc_start: 0.8758 (m-80) cc_final: 0.8443 (m-80) REVERT: A 425 MET cc_start: 0.9251 (mmp) cc_final: 0.8796 (mmm) REVERT: C 77 GLU cc_start: 0.9261 (mp0) cc_final: 0.9059 (mp0) REVERT: C 202 PHE cc_start: 0.9154 (m-80) cc_final: 0.8626 (m-80) REVERT: C 253 THR cc_start: 0.9374 (m) cc_final: 0.9116 (p) REVERT: C 313 MET cc_start: 0.6188 (mmp) cc_final: 0.4310 (mmp) REVERT: G 73 THR cc_start: 0.8652 (m) cc_final: 0.8341 (m) REVERT: G 77 GLU cc_start: 0.9301 (mm-30) cc_final: 0.9046 (mm-30) REVERT: G 137 VAL cc_start: 0.9347 (t) cc_final: 0.9063 (p) REVERT: G 157 LEU cc_start: 0.9257 (mt) cc_final: 0.9025 (mt) REVERT: G 169 PHE cc_start: 0.9427 (m-80) cc_final: 0.8773 (m-80) REVERT: G 199 ASP cc_start: 0.9546 (m-30) cc_final: 0.9075 (t0) REVERT: G 313 MET cc_start: 0.6448 (mmp) cc_final: 0.5123 (mmp) REVERT: G 319 TYR cc_start: 0.9414 (m-10) cc_final: 0.9125 (m-80) REVERT: E 205 ASP cc_start: 0.7434 (t0) cc_final: 0.6680 (m-30) REVERT: E 255 PHE cc_start: 0.8826 (m-80) cc_final: 0.8312 (m-80) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.4001 time to fit residues: 266.0017 Evaluate side-chains 395 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: [129, 9, 112, 43, 19, 262, 60, 28, 188, 263, 205] chunk 129 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 112 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 262 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 188 optimal weight: 20.0000 chunk 263 optimal weight: 3.9990 chunk 205 optimal weight: 30.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 124 ASN ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.085363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.063259 restraints weight = 353496.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.067342 restraints weight = 224255.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.070545 restraints weight = 153510.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.073065 restraints weight = 110718.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.075001 restraints weight = 82998.606| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.8416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 22308 Z= 0.192 Angle : 0.608 20.500 30216 Z= 0.340 Chirality : 0.042 0.231 3305 Planarity : 0.007 0.217 3960 Dihedral : 5.088 54.428 3010 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.91 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2752 helix: 0.92 (0.14), residues: 1255 sheet: -0.93 (0.25), residues: 374 loop : -0.53 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 221 TYR 0.019 0.002 TYR G 224 PHE 0.047 0.002 PHE D 408 TRP 0.016 0.001 TRP B 344 HIS 0.010 0.002 HIS G 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 (22292) covalent geometry : angle 0.60773 / 0.34 (30216) hydrogen bonds : bond 0.05146 / 3.25 ( 1125) hydrogen bonds : angle 5.01341 / 3.58 ( 3213) Misc. bond : bond 0.01344 / 0.84 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 MET cc_start: 0.9801 (tpt) cc_final: 0.9349 (tpp) REVERT: J 65 LEU cc_start: 0.8569 (tp) cc_final: 0.7993 (tt) REVERT: J 70 PHE cc_start: 0.8904 (t80) cc_final: 0.8041 (t80) REVERT: J 74 PHE cc_start: 0.8900 (m-10) cc_final: 0.8100 (m-10) REVERT: J 94 TYR cc_start: 0.9302 (t80) cc_final: 0.8717 (t80) REVERT: J 129 PHE cc_start: 0.9648 (t80) cc_final: 0.9407 (t80) REVERT: B 105 HIS cc_start: 0.9013 (t70) cc_final: 0.8770 (t70) REVERT: B 167 PHE cc_start: 0.9021 (m-10) cc_final: 0.8529 (m-80) REVERT: B 200 TYR cc_start: 0.9074 (m-80) cc_final: 0.8561 (m-80) REVERT: B 201 CYS cc_start: 0.8311 (m) cc_final: 0.7542 (p) REVERT: B 203 ASP cc_start: 0.7028 (t0) cc_final: 0.6368 (m-30) REVERT: B 298 ASN cc_start: 0.9570 (m110) cc_final: 0.9179 (t0) REVERT: B 345 ILE cc_start: 0.8029 (mm) cc_final: 0.7822 (mm) REVERT: D 128 ASP cc_start: 0.8161 (m-30) cc_final: 0.7934 (m-30) REVERT: D 165 ASN cc_start: 0.9494 (t0) cc_final: 0.9217 (t0) REVERT: D 265 PHE cc_start: 0.9503 (m-80) cc_final: 0.9083 (m-80) REVERT: D 418 LEU cc_start: 0.9247 (tp) cc_final: 0.8942 (tp) REVERT: A 169 PHE cc_start: 0.9171 (m-80) cc_final: 0.8849 (m-80) REVERT: A 202 PHE cc_start: 0.8741 (m-80) cc_final: 0.8435 (m-80) REVERT: A 267 PHE cc_start: 0.8553 (m-80) cc_final: 0.8192 (m-80) REVERT: A 425 MET cc_start: 0.9294 (mmp) cc_final: 0.8879 (mmm) REVERT: C 253 THR cc_start: 0.9375 (m) cc_final: 0.9117 (p) REVERT: G 73 THR cc_start: 0.8633 (m) cc_final: 0.8278 (m) REVERT: G 77 GLU cc_start: 0.9297 (mm-30) cc_final: 0.9055 (mm-30) REVERT: G 137 VAL cc_start: 0.9353 (t) cc_final: 0.9082 (p) REVERT: G 169 PHE cc_start: 0.9424 (m-80) cc_final: 0.8767 (m-80) REVERT: G 199 ASP cc_start: 0.9551 (m-30) cc_final: 0.9131 (t0) REVERT: G 313 MET cc_start: 0.6563 (mmp) cc_final: 0.5244 (mmp) REVERT: G 319 TYR cc_start: 0.9422 (m-10) cc_final: 0.9077 (m-80) REVERT: E 205 ASP cc_start: 0.7364 (t0) cc_final: 0.6615 (m-30) REVERT: E 255 PHE cc_start: 0.8797 (m-80) cc_final: 0.8285 (m-80) REVERT: E 358 GLU cc_start: 0.9210 (tp30) cc_final: 0.8819 (mt-10) REVERT: E 386 GLU cc_start: 0.9263 (mp0) cc_final: 0.9049 (mp0) outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.3899 time to fit residues: 256.8936 Evaluate side-chains 391 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: [228, 43, 210, 251, 35, 132, 86, 241, 225, 51, 159] chunk 228 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 210 optimal weight: 9.9990 chunk 251 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 241 optimal weight: 0.7980 chunk 225 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 overall best weight: 7.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 29 HIS ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN ** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN E 186 ASN ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.083432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.061856 restraints weight = 353907.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.065834 restraints weight = 223160.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.069002 restraints weight = 152071.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.071498 restraints weight = 109024.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.073405 restraints weight = 81606.467| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.8799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 22308 Z= 0.221 Angle : 0.639 20.243 30216 Z= 0.361 Chirality : 0.042 0.228 3305 Planarity : 0.008 0.219 3960 Dihedral : 5.225 54.937 3010 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.31 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.16), residues: 2752 helix: 0.75 (0.14), residues: 1249 sheet: -1.02 (0.25), residues: 374 loop : -0.63 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 221 TYR 0.025 0.002 TYR E 210 PHE 0.021 0.002 PHE B 341 TRP 0.015 0.002 TRP B 344 HIS 0.010 0.002 HIS G 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.22 (22292) covalent geometry : angle 0.63903 / 0.36 (30216) hydrogen bonds : bond 0.05260 / 3.34 ( 1125) hydrogen bonds : angle 5.15561 / 3.68 ( 3213) Misc. bond : bond 0.01375 / 0.86 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5504 Ramachandran restraints generated. 2752 Oldfield, 0 Emsley, 2752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 58 MET cc_start: 0.9797 (tpt) cc_final: 0.9370 (tpp) REVERT: J 65 LEU cc_start: 0.8651 (tp) cc_final: 0.8141 (tt) REVERT: J 70 PHE cc_start: 0.8938 (t80) cc_final: 0.8145 (t80) REVERT: J 74 PHE cc_start: 0.8944 (m-10) cc_final: 0.8257 (m-10) REVERT: J 94 TYR cc_start: 0.9361 (t80) cc_final: 0.8814 (t80) REVERT: J 129 PHE cc_start: 0.9674 (t80) cc_final: 0.9396 (t80) REVERT: B 67 ASP cc_start: 0.6996 (t0) cc_final: 0.5814 (p0) REVERT: B 105 HIS cc_start: 0.9085 (t70) cc_final: 0.8849 (t70) REVERT: B 167 PHE cc_start: 0.9090 (m-10) cc_final: 0.8741 (m-80) REVERT: B 200 TYR cc_start: 0.9088 (m-80) cc_final: 0.8886 (m-80) REVERT: B 201 CYS cc_start: 0.8325 (m) cc_final: 0.8113 (m) REVERT: B 203 ASP cc_start: 0.7132 (t0) cc_final: 0.6580 (m-30) REVERT: B 298 ASN cc_start: 0.9588 (m110) cc_final: 0.9176 (t0) REVERT: D 128 ASP cc_start: 0.8194 (m-30) cc_final: 0.7951 (m-30) REVERT: D 165 ASN cc_start: 0.9517 (t0) cc_final: 0.9260 (t0) REVERT: D 265 PHE cc_start: 0.9550 (m-80) cc_final: 0.9160 (m-80) REVERT: D 330 MET cc_start: 0.9260 (ttt) cc_final: 0.8951 (tpp) REVERT: D 418 LEU cc_start: 0.9262 (tp) cc_final: 0.8975 (tp) REVERT: A 169 PHE cc_start: 0.9218 (m-80) cc_final: 0.8929 (m-80) REVERT: A 202 PHE cc_start: 0.8737 (m-80) cc_final: 0.8419 (m-80) REVERT: A 267 PHE cc_start: 0.8590 (m-80) cc_final: 0.8267 (m-80) REVERT: A 425 MET cc_start: 0.9312 (mmp) cc_final: 0.8893 (mmm) REVERT: C 202 PHE cc_start: 0.9088 (m-80) cc_final: 0.8514 (m-80) REVERT: C 253 THR cc_start: 0.9360 (m) cc_final: 0.9106 (p) REVERT: G 73 THR cc_start: 0.8820 (m) cc_final: 0.8522 (p) REVERT: G 77 GLU cc_start: 0.9306 (mm-30) cc_final: 0.9064 (mm-30) REVERT: G 137 VAL cc_start: 0.9360 (t) cc_final: 0.9084 (p) REVERT: G 169 PHE cc_start: 0.9449 (m-80) cc_final: 0.8809 (m-80) REVERT: G 199 ASP cc_start: 0.9520 (m-30) cc_final: 0.9095 (t0) REVERT: G 313 MET cc_start: 0.6796 (mmp) cc_final: 0.5406 (mmp) REVERT: G 319 TYR cc_start: 0.9420 (m-10) cc_final: 0.9062 (m-80) REVERT: E 205 ASP cc_start: 0.7294 (t0) cc_final: 0.6550 (m-30) REVERT: E 255 PHE cc_start: 0.8891 (m-80) cc_final: 0.8355 (m-80) REVERT: E 358 GLU cc_start: 0.9217 (tp30) cc_final: 0.8854 (mt-10) outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.3943 time to fit residues: 259.8392 Evaluate side-chains 388 residues out of total 2353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: [52, 62, 64, 119, 87, 253, 258, 152, 91, 186, 81] chunk 52 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 253 optimal weight: 20.0000 chunk 258 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 186 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 29 HIS ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.083745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.062142 restraints weight = 357426.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.066149 restraints weight = 225239.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.069344 restraints weight = 153450.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.071811 restraints weight = 110244.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.073729 restraints weight = 82527.249| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 0.8999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 22308 Z= 0.183 Angle : 0.596 20.219 30216 Z= 0.334 Chirality : 0.042 0.228 3305 Planarity : 0.007 0.218 3960 Dihedral : 5.111 55.552 3010 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.76 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.16), residues: 2752 helix: 1.00 (0.14), residues: 1255 sheet: -0.99 (0.25), residues: 374 loop : -0.58 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 221 TYR 0.018 0.002 TYR G 210 PHE 0.020 0.002 PHE C 351 TRP 0.013 0.001 TRP B 344 HIS 0.010 0.001 HIS B 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.18 (22292) covalent geometry : angle 0.59619 / 0.33 (30216) hydrogen bonds : bond 0.05117 / 3.23 ( 1125) hydrogen bonds : angle 5.00052 / 3.57 ( 3213) Misc. bond : bond 0.01392 / 0.86 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7396.34 seconds wall clock time: 127 minutes 4.58 seconds (7624.58 seconds total)