Starting phenix.real_space_refine on Sun Apr 5 22:08:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rgm_53950/04_2026/9rgm_53950.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rgm_53950/04_2026/9rgm_53950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rgm_53950/04_2026/9rgm_53950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rgm_53950/04_2026/9rgm_53950.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rgm_53950/04_2026/9rgm_53950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rgm_53950/04_2026/9rgm_53950.map" } resolution = 4.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 85 5.16 5 C 8900 2.51 5 N 2235 2.21 5 O 2405 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13625 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2725 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 313} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.43, per 1000 atoms: 0.18 Number of scatterers: 13625 At special positions: 0 Unit cell: (95.0625, 97.2562, 123.581, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 85 16.00 O 2405 8.00 N 2235 7.00 C 8900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 115 " distance=2.08 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 145 " distance=2.08 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 115 " distance=2.08 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 115 " distance=2.08 Simple disulfide: pdb=" SG CYS D 69 " - pdb=" SG CYS D 115 " distance=2.08 Simple disulfide: pdb=" SG CYS E 69 " - pdb=" SG CYS E 115 " distance=2.08 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 145 " distance=2.08 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 145 " distance=2.08 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 145 " distance=2.08 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 145 " distance=2.08 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 422.0 milliseconds 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 15 sheets defined 32.7% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 78 through 83 removed outlier: 4.273A pdb=" N GLU A 82 " --> pdb=" O HIS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 234 removed outlier: 3.689A pdb=" N ILE A 217 " --> pdb=" O PHE A 213 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 219 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.721A pdb=" N ARG A 245 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 261 removed outlier: 3.556A pdb=" N LYS A 261 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 Processing helix chain 'A' and resid 274 through 303 removed outlier: 3.696A pdb=" N LEU A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 333 Proline residue: A 321 - end of helix Processing helix chain 'B' and resid 78 through 83 removed outlier: 4.276A pdb=" N GLU B 82 " --> pdb=" O HIS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 234 removed outlier: 3.690A pdb=" N ILE B 217 " --> pdb=" O PHE B 213 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 219 " --> pdb=" O TYR B 215 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.721A pdb=" N ARG B 245 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL B 246 " --> pdb=" O PRO B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 removed outlier: 3.557A pdb=" N LYS B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 Processing helix chain 'B' and resid 274 through 303 removed outlier: 3.696A pdb=" N LEU B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 333 Proline residue: B 321 - end of helix Processing helix chain 'C' and resid 78 through 83 removed outlier: 4.275A pdb=" N GLU C 82 " --> pdb=" O HIS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 234 removed outlier: 3.690A pdb=" N ILE C 217 " --> pdb=" O PHE C 213 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU C 218 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 219 " --> pdb=" O TYR C 215 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 241 through 246 removed outlier: 3.721A pdb=" N ARG C 245 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 261 removed outlier: 3.557A pdb=" N LYS C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 265 Processing helix chain 'C' and resid 274 through 303 removed outlier: 3.697A pdb=" N LEU C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 333 Proline residue: C 321 - end of helix Processing helix chain 'D' and resid 78 through 83 removed outlier: 4.275A pdb=" N GLU D 82 " --> pdb=" O HIS D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 234 removed outlier: 3.688A pdb=" N ILE D 217 " --> pdb=" O PHE D 213 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU D 218 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL D 219 " --> pdb=" O TYR D 215 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 241 through 246 removed outlier: 3.721A pdb=" N ARG D 245 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL D 246 " --> pdb=" O PRO D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 261 removed outlier: 3.557A pdb=" N LYS D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 265 Processing helix chain 'D' and resid 274 through 303 removed outlier: 3.696A pdb=" N LEU D 278 " --> pdb=" O LYS D 274 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE D 288 " --> pdb=" O ILE D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 333 Proline residue: D 321 - end of helix Processing helix chain 'E' and resid 78 through 83 removed outlier: 4.274A pdb=" N GLU E 82 " --> pdb=" O HIS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 234 removed outlier: 3.690A pdb=" N ILE E 217 " --> pdb=" O PHE E 213 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL E 219 " --> pdb=" O TYR E 215 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU E 222 " --> pdb=" O LEU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 241 through 246 removed outlier: 3.722A pdb=" N ARG E 245 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL E 246 " --> pdb=" O PRO E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 261 removed outlier: 3.557A pdb=" N LYS E 261 " --> pdb=" O VAL E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 265 Processing helix chain 'E' and resid 274 through 303 removed outlier: 3.696A pdb=" N LEU E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL E 285 " --> pdb=" O ALA E 281 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE E 288 " --> pdb=" O ILE E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 333 Proline residue: E 321 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.280A pdb=" N ILE A 52 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 54 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A 121 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP A 60 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 119 " --> pdb=" O TRP A 60 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HIS A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ARG A 124 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU A 108 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ASN A 126 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR A 106 " --> pdb=" O ASN A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 5.373A pdb=" N PHE A 61 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL A 30 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.540A pdb=" N CYS A 145 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 147 " --> pdb=" O VAL A 205 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 198 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU A 192 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR A 200 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP A 190 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA A 202 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLN A 188 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N PHE A 204 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL A 186 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N HIS A 206 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR A 184 " --> pdb=" O HIS A 206 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS A 208 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 42 through 44 removed outlier: 4.277A pdb=" N ILE B 52 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 54 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET B 121 " --> pdb=" O TYR B 58 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP B 60 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 119 " --> pdb=" O TRP B 60 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N HIS B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG B 124 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU B 108 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASN B 126 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR B 106 " --> pdb=" O ASN B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 42 through 44 removed outlier: 5.372A pdb=" N PHE B 61 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL B 30 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.540A pdb=" N CYS B 145 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 147 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU B 198 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU B 192 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR B 200 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP B 190 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA B 202 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLN B 188 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N PHE B 204 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL B 186 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N HIS B 206 " --> pdb=" O TYR B 184 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N TYR B 184 " --> pdb=" O HIS B 206 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS B 208 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 44 removed outlier: 4.279A pdb=" N ILE C 52 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C 54 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET C 121 " --> pdb=" O TYR C 58 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP C 60 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL C 119 " --> pdb=" O TRP C 60 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N HIS C 118 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG C 124 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU C 108 " --> pdb=" O ARG C 124 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ASN C 126 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR C 106 " --> pdb=" O ASN C 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 42 through 44 removed outlier: 5.373A pdb=" N PHE C 61 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL C 30 " --> pdb=" O PHE C 61 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.540A pdb=" N CYS C 145 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE C 147 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU C 198 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU C 192 " --> pdb=" O GLU C 198 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N TYR C 200 " --> pdb=" O ASP C 190 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP C 190 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA C 202 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN C 188 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE C 204 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL C 186 " --> pdb=" O PHE C 204 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N HIS C 206 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR C 184 " --> pdb=" O HIS C 206 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS C 208 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 42 through 44 removed outlier: 4.276A pdb=" N ILE D 52 " --> pdb=" O LEU D 127 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA D 54 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET D 121 " --> pdb=" O TYR D 58 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP D 60 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 119 " --> pdb=" O TRP D 60 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N HIS D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG D 124 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU D 108 " --> pdb=" O ARG D 124 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASN D 126 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR D 106 " --> pdb=" O ASN D 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 42 through 44 removed outlier: 5.374A pdb=" N PHE D 61 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL D 30 " --> pdb=" O PHE D 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 90 through 91 removed outlier: 3.540A pdb=" N CYS D 145 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE D 147 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU D 198 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLU D 192 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR D 200 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP D 190 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA D 202 " --> pdb=" O GLN D 188 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLN D 188 " --> pdb=" O ALA D 202 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N PHE D 204 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL D 186 " --> pdb=" O PHE D 204 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N HIS D 206 " --> pdb=" O TYR D 184 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR D 184 " --> pdb=" O HIS D 206 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS D 208 " --> pdb=" O LYS D 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 42 through 44 removed outlier: 4.277A pdb=" N ILE E 52 " --> pdb=" O LEU E 127 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA E 54 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET E 121 " --> pdb=" O TYR E 58 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TRP E 60 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL E 119 " --> pdb=" O TRP E 60 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N HIS E 118 " --> pdb=" O ASP E 114 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG E 124 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU E 108 " --> pdb=" O ARG E 124 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASN E 126 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR E 106 " --> pdb=" O ASN E 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 42 through 44 removed outlier: 5.374A pdb=" N PHE E 61 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL E 30 " --> pdb=" O PHE E 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 90 through 91 removed outlier: 3.540A pdb=" N CYS E 145 " --> pdb=" O LEU E 207 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 147 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU E 198 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLU E 192 " --> pdb=" O GLU E 198 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR E 200 " --> pdb=" O ASP E 190 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ASP E 190 " --> pdb=" O TYR E 200 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ALA E 202 " --> pdb=" O GLN E 188 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLN E 188 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE E 204 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL E 186 " --> pdb=" O PHE E 204 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N HIS E 206 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR E 184 " --> pdb=" O HIS E 206 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS E 208 " --> pdb=" O LYS E 182 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3116 1.33 - 1.46: 4055 1.46 - 1.58: 6684 1.58 - 1.70: 0 1.70 - 1.82: 125 Bond restraints: 13980 Sorted by residual: bond pdb=" CA SER D 125 " pdb=" CB SER D 125 " ideal model delta sigma weight residual 1.533 1.451 0.082 1.72e-02 3.38e+03 2.25e+01 bond pdb=" CA SER C 125 " pdb=" CB SER C 125 " ideal model delta sigma weight residual 1.533 1.451 0.081 1.72e-02 3.38e+03 2.24e+01 bond pdb=" CA SER E 125 " pdb=" CB SER E 125 " ideal model delta sigma weight residual 1.533 1.451 0.081 1.72e-02 3.38e+03 2.23e+01 bond pdb=" CA SER A 125 " pdb=" CB SER A 125 " ideal model delta sigma weight residual 1.533 1.452 0.081 1.72e-02 3.38e+03 2.21e+01 bond pdb=" CA SER B 125 " pdb=" CB SER B 125 " ideal model delta sigma weight residual 1.533 1.452 0.081 1.72e-02 3.38e+03 2.19e+01 ... (remaining 13975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 16433 2.55 - 5.09: 2209 5.09 - 7.64: 268 7.64 - 10.19: 55 10.19 - 12.73: 10 Bond angle restraints: 18975 Sorted by residual: angle pdb=" N GLN D 55 " pdb=" CA GLN D 55 " pdb=" CB GLN D 55 " ideal model delta sigma weight residual 111.08 98.35 12.73 1.71e+00 3.42e-01 5.55e+01 angle pdb=" N GLN A 55 " pdb=" CA GLN A 55 " pdb=" CB GLN A 55 " ideal model delta sigma weight residual 111.08 98.36 12.72 1.71e+00 3.42e-01 5.53e+01 angle pdb=" N GLN E 55 " pdb=" CA GLN E 55 " pdb=" CB GLN E 55 " ideal model delta sigma weight residual 111.08 98.39 12.69 1.71e+00 3.42e-01 5.51e+01 angle pdb=" N GLN C 55 " pdb=" CA GLN C 55 " pdb=" CB GLN C 55 " ideal model delta sigma weight residual 111.08 98.41 12.67 1.71e+00 3.42e-01 5.49e+01 angle pdb=" N GLN B 55 " pdb=" CA GLN B 55 " pdb=" CB GLN B 55 " ideal model delta sigma weight residual 111.08 98.45 12.63 1.71e+00 3.42e-01 5.46e+01 ... (remaining 18970 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.63: 6995 13.63 - 27.25: 1017 27.25 - 40.88: 198 40.88 - 54.51: 60 54.51 - 68.13: 40 Dihedral angle restraints: 8310 sinusoidal: 3425 harmonic: 4885 Sorted by residual: dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 145 " pdb=" CB CYS C 145 " ideal model delta sinusoidal sigma weight residual -86.00 -148.71 62.71 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 145 " pdb=" CB CYS A 145 " ideal model delta sinusoidal sigma weight residual -86.00 -148.67 62.67 1 1.00e+01 1.00e-02 5.19e+01 dihedral pdb=" CB CYS E 131 " pdb=" SG CYS E 131 " pdb=" SG CYS E 145 " pdb=" CB CYS E 145 " ideal model delta sinusoidal sigma weight residual -86.00 -148.62 62.62 1 1.00e+01 1.00e-02 5.19e+01 ... (remaining 8307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1079 0.062 - 0.125: 717 0.125 - 0.187: 243 0.187 - 0.249: 61 0.249 - 0.312: 25 Chirality restraints: 2125 Sorted by residual: chirality pdb=" CA PRO D 195 " pdb=" N PRO D 195 " pdb=" C PRO D 195 " pdb=" CB PRO D 195 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA PRO C 195 " pdb=" N PRO C 195 " pdb=" C PRO C 195 " pdb=" CB PRO C 195 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA PRO A 195 " pdb=" N PRO A 195 " pdb=" C PRO A 195 " pdb=" CB PRO A 195 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 2122 not shown) Planarity restraints: 2360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 158 " 0.465 9.50e-02 1.11e+02 2.09e-01 3.00e+01 pdb=" NE ARG E 158 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG E 158 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG E 158 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG E 158 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 158 " 0.465 9.50e-02 1.11e+02 2.09e-01 3.00e+01 pdb=" NE ARG D 158 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG D 158 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG D 158 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG D 158 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 158 " 0.465 9.50e-02 1.11e+02 2.09e-01 2.99e+01 pdb=" NE ARG C 158 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG C 158 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG C 158 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 158 " 0.026 2.00e-02 2.50e+03 ... (remaining 2357 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3139 2.80 - 3.33: 12941 3.33 - 3.85: 20174 3.85 - 4.38: 22294 4.38 - 4.90: 38514 Nonbonded interactions: 97062 Sorted by model distance: nonbonded pdb=" OE2 GLU C 57 " pdb=" CD ARG C 122 " model vdw 2.281 3.440 nonbonded pdb=" OE2 GLU B 57 " pdb=" CD ARG B 122 " model vdw 2.281 3.440 nonbonded pdb=" OE2 GLU D 57 " pdb=" CD ARG D 122 " model vdw 2.281 3.440 nonbonded pdb=" OE2 GLU E 57 " pdb=" CD ARG E 122 " model vdw 2.282 3.440 nonbonded pdb=" OE2 GLU A 57 " pdb=" CD ARG A 122 " model vdw 2.287 3.440 ... (remaining 97057 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.310 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.082 13990 Z= 0.627 Angle : 1.814 12.734 18995 Z= 1.150 Chirality : 0.091 0.312 2125 Planarity : 0.018 0.209 2360 Dihedral : 14.215 68.132 5090 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.98 % Allowed : 9.45 % Favored : 89.58 % Cbeta Deviations : 1.88 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % 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: -2.62 (0.18), residues: 1600 helix: -2.08 (0.20), residues: 400 sheet: -1.52 (0.23), residues: 375 loop : -1.57 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.005 ARG E 158 TYR 0.052 0.007 TYR B 135 PHE 0.030 0.007 PHE C 221 TRP 0.028 0.005 TRP D 163 HIS 0.011 0.003 HIS D 187 Details of bonding type rmsd covalent geometry : bond 0.01015 (13980) covalent geometry : angle 1.80812 (18975) SS BOND : bond 0.04722 ( 10) SS BOND : angle 4.90835 ( 20) hydrogen bonds : bond 0.26316 ( 500) hydrogen bonds : angle 7.98518 ( 1425) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 287 time to evaluate : 0.516 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: A 128 ASP cc_start: 0.9273 (t0) cc_final: 0.8463 (p0) REVERT: A 232 TRP cc_start: 0.8278 (t60) cc_final: 0.8040 (t60) REVERT: A 262 GLU cc_start: 0.9263 (tt0) cc_final: 0.8967 (tm-30) REVERT: B 128 ASP cc_start: 0.9216 (t0) cc_final: 0.8454 (p0) REVERT: B 133 MET cc_start: 0.9291 (mtt) cc_final: 0.8856 (mtt) REVERT: B 232 TRP cc_start: 0.8293 (t60) cc_final: 0.8065 (t60) REVERT: B 266 ASN cc_start: 0.8793 (t0) cc_final: 0.8581 (t0) REVERT: B 288 PHE cc_start: 0.9590 (t80) cc_final: 0.9377 (t80) REVERT: C 128 ASP cc_start: 0.9220 (t0) cc_final: 0.8439 (p0) REVERT: C 133 MET cc_start: 0.9311 (mtt) cc_final: 0.9064 (mtt) REVERT: C 262 GLU cc_start: 0.9306 (tt0) cc_final: 0.9033 (tm-30) REVERT: C 266 ASN cc_start: 0.8828 (t0) cc_final: 0.8626 (t0) REVERT: D 128 ASP cc_start: 0.9229 (t0) cc_final: 0.8489 (p0) REVERT: D 133 MET cc_start: 0.9318 (mtt) cc_final: 0.8878 (mtt) REVERT: D 232 TRP cc_start: 0.8308 (t60) cc_final: 0.8058 (t60) REVERT: D 262 GLU cc_start: 0.9247 (tt0) cc_final: 0.8958 (tm-30) REVERT: E 128 ASP cc_start: 0.9228 (t0) cc_final: 0.8457 (p0) REVERT: E 133 MET cc_start: 0.9315 (mtt) cc_final: 0.8889 (mtt) REVERT: E 262 GLU cc_start: 0.9291 (tt0) cc_final: 0.9024 (tm-30) outliers start: 15 outliers final: 15 residues processed: 302 average time/residue: 0.1075 time to fit residues: 48.0591 Evaluate side-chains 208 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 331 HIS B 328 ASN B 331 HIS C 328 ASN C 331 HIS D 328 ASN D 331 HIS E 328 ASN E 331 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.113821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.084483 restraints weight = 40686.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.087063 restraints weight = 23644.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.088791 restraints weight = 16824.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.089753 restraints weight = 13559.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.090445 restraints weight = 11941.476| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13990 Z= 0.186 Angle : 0.727 7.490 18995 Z= 0.387 Chirality : 0.047 0.184 2125 Planarity : 0.004 0.041 2360 Dihedral : 7.128 29.550 1790 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.18), residues: 1600 helix: -0.73 (0.22), residues: 405 sheet: -1.30 (0.22), residues: 415 loop : -1.24 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 317 TYR 0.011 0.002 TYR E 200 PHE 0.028 0.002 PHE A 288 TRP 0.022 0.002 TRP C 232 HIS 0.003 0.001 HIS D 331 Details of bonding type rmsd covalent geometry : bond 0.00377 (13980) covalent geometry : angle 0.72742 (18975) SS BOND : bond 0.01487 ( 10) SS BOND : angle 0.64809 ( 20) hydrogen bonds : bond 0.06574 ( 500) hydrogen bonds : angle 5.56199 ( 1425) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 234 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.8474 (t0) cc_final: 0.7890 (p0) REVERT: A 226 PHE cc_start: 0.8727 (m-10) cc_final: 0.8372 (m-10) REVERT: B 128 ASP cc_start: 0.8278 (t0) cc_final: 0.7807 (p0) REVERT: B 226 PHE cc_start: 0.8698 (m-10) cc_final: 0.8494 (m-10) REVERT: C 128 ASP cc_start: 0.8427 (t0) cc_final: 0.7976 (p0) REVERT: C 226 PHE cc_start: 0.8724 (m-10) cc_final: 0.8461 (m-10) REVERT: D 128 ASP cc_start: 0.8406 (t0) cc_final: 0.7950 (p0) REVERT: D 226 PHE cc_start: 0.8726 (m-10) cc_final: 0.8303 (m-10) REVERT: E 128 ASP cc_start: 0.8318 (t0) cc_final: 0.7844 (p0) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.0928 time to fit residues: 34.1219 Evaluate side-chains 179 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 29 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 117 optimal weight: 0.3980 chunk 91 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 HIS B 331 HIS C 331 HIS D 331 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.110271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.080823 restraints weight = 40216.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.083303 restraints weight = 23583.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.084923 restraints weight = 16649.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.085844 restraints weight = 13421.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.086552 restraints weight = 11831.507| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13990 Z= 0.189 Angle : 0.682 6.817 18995 Z= 0.362 Chirality : 0.046 0.193 2125 Planarity : 0.004 0.032 2360 Dihedral : 6.609 27.264 1790 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.26 % Allowed : 2.41 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.19), residues: 1600 helix: 0.17 (0.25), residues: 380 sheet: -1.35 (0.22), residues: 430 loop : -1.15 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 245 TYR 0.013 0.002 TYR C 272 PHE 0.015 0.002 PHE E 226 TRP 0.024 0.002 TRP D 232 HIS 0.003 0.001 HIS D 331 Details of bonding type rmsd covalent geometry : bond 0.00425 (13980) covalent geometry : angle 0.68172 (18975) SS BOND : bond 0.00344 ( 10) SS BOND : angle 0.50595 ( 20) hydrogen bonds : bond 0.05814 ( 500) hydrogen bonds : angle 5.16399 ( 1425) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 213 time to evaluate : 0.514 Fit side-chains REVERT: A 128 ASP cc_start: 0.8551 (t0) cc_final: 0.7821 (p0) REVERT: A 226 PHE cc_start: 0.8735 (m-10) cc_final: 0.8424 (m-10) REVERT: A 232 TRP cc_start: 0.8509 (t60) cc_final: 0.7947 (t60) REVERT: B 128 ASP cc_start: 0.8419 (t0) cc_final: 0.7863 (p0) REVERT: C 128 ASP cc_start: 0.8477 (t0) cc_final: 0.7933 (p0) REVERT: D 128 ASP cc_start: 0.8481 (t0) cc_final: 0.7899 (p0) REVERT: D 226 PHE cc_start: 0.8732 (m-10) cc_final: 0.8404 (m-10) REVERT: D 229 LEU cc_start: 0.9419 (tp) cc_final: 0.9173 (mt) REVERT: D 232 TRP cc_start: 0.8489 (t60) cc_final: 0.7925 (t60) REVERT: E 128 ASP cc_start: 0.8441 (t0) cc_final: 0.7849 (p0) outliers start: 4 outliers final: 0 residues processed: 213 average time/residue: 0.0871 time to fit residues: 29.9593 Evaluate side-chains 161 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 157 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 41 optimal weight: 0.2980 chunk 16 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 HIS B 331 HIS C 331 HIS E 331 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.111079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.081183 restraints weight = 40641.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.083666 restraints weight = 24072.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.085341 restraints weight = 17258.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.086243 restraints weight = 14035.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.086968 restraints weight = 12446.742| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13990 Z= 0.179 Angle : 0.648 7.110 18995 Z= 0.342 Chirality : 0.046 0.161 2125 Planarity : 0.003 0.028 2360 Dihedral : 6.321 26.797 1790 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.19), residues: 1600 helix: 0.54 (0.26), residues: 380 sheet: -1.47 (0.22), residues: 430 loop : -1.21 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 158 TYR 0.010 0.001 TYR E 200 PHE 0.012 0.002 PHE E 123 TRP 0.021 0.002 TRP A 232 HIS 0.004 0.001 HIS C 331 Details of bonding type rmsd covalent geometry : bond 0.00407 (13980) covalent geometry : angle 0.64799 (18975) SS BOND : bond 0.00213 ( 10) SS BOND : angle 0.42618 ( 20) hydrogen bonds : bond 0.05098 ( 500) hydrogen bonds : angle 4.81149 ( 1425) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.8508 (t0) cc_final: 0.7781 (p0) REVERT: B 128 ASP cc_start: 0.8448 (t0) cc_final: 0.7841 (p0) REVERT: C 128 ASP cc_start: 0.8480 (t0) cc_final: 0.7830 (p0) REVERT: D 128 ASP cc_start: 0.8504 (t0) cc_final: 0.7808 (p0) REVERT: E 128 ASP cc_start: 0.8435 (t0) cc_final: 0.7877 (p0) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.0784 time to fit residues: 26.8146 Evaluate side-chains 155 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.080613 restraints weight = 40617.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.083023 restraints weight = 23979.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.084616 restraints weight = 17211.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.085584 restraints weight = 13975.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.086065 restraints weight = 12321.276| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13990 Z= 0.195 Angle : 0.665 7.158 18995 Z= 0.349 Chirality : 0.046 0.163 2125 Planarity : 0.003 0.039 2360 Dihedral : 6.255 26.504 1790 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.19), residues: 1600 helix: 0.77 (0.26), residues: 380 sheet: -1.62 (0.22), residues: 430 loop : -1.16 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 93 TYR 0.015 0.001 TYR B 200 PHE 0.013 0.002 PHE B 123 TRP 0.008 0.001 TRP A 279 HIS 0.009 0.001 HIS C 331 Details of bonding type rmsd covalent geometry : bond 0.00446 (13980) covalent geometry : angle 0.66478 (18975) SS BOND : bond 0.00168 ( 10) SS BOND : angle 0.48982 ( 20) hydrogen bonds : bond 0.05066 ( 500) hydrogen bonds : angle 4.74866 ( 1425) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.526 Fit side-chains REVERT: A 128 ASP cc_start: 0.8463 (t0) cc_final: 0.7785 (p0) REVERT: A 176 MET cc_start: 0.8814 (ttp) cc_final: 0.8600 (ttm) REVERT: B 128 ASP cc_start: 0.8405 (t0) cc_final: 0.7872 (p0) REVERT: C 128 ASP cc_start: 0.8374 (t0) cc_final: 0.7813 (p0) REVERT: D 128 ASP cc_start: 0.8452 (t0) cc_final: 0.7848 (p0) REVERT: E 128 ASP cc_start: 0.8369 (t0) cc_final: 0.8077 (p0) REVERT: E 176 MET cc_start: 0.8894 (ttm) cc_final: 0.8677 (ttm) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.0804 time to fit residues: 27.8954 Evaluate side-chains 153 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 99 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.111594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.082802 restraints weight = 37671.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.084846 restraints weight = 23899.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.085947 restraints weight = 17132.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.086308 restraints weight = 14458.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.086447 restraints weight = 13474.164| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13990 Z= 0.140 Angle : 0.618 7.111 18995 Z= 0.325 Chirality : 0.046 0.232 2125 Planarity : 0.003 0.032 2360 Dihedral : 6.021 25.764 1790 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.20), residues: 1600 helix: 1.03 (0.26), residues: 380 sheet: -1.59 (0.21), residues: 460 loop : -1.01 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 158 TYR 0.019 0.001 TYR B 200 PHE 0.023 0.001 PHE B 324 TRP 0.033 0.002 TRP D 60 HIS 0.002 0.001 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00314 (13980) covalent geometry : angle 0.61778 (18975) SS BOND : bond 0.00717 ( 10) SS BOND : angle 1.06696 ( 20) hydrogen bonds : bond 0.04557 ( 500) hydrogen bonds : angle 4.47808 ( 1425) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.8429 (t0) cc_final: 0.7779 (p0) REVERT: B 128 ASP cc_start: 0.8360 (t0) cc_final: 0.7838 (p0) REVERT: C 128 ASP cc_start: 0.8469 (t0) cc_final: 0.7870 (p0) REVERT: C 154 MET cc_start: 0.8695 (mmm) cc_final: 0.8466 (mmm) REVERT: D 128 ASP cc_start: 0.8431 (t0) cc_final: 0.7834 (p0) REVERT: D 154 MET cc_start: 0.8800 (mmm) cc_final: 0.8593 (mmm) REVERT: E 128 ASP cc_start: 0.8344 (t0) cc_final: 0.8015 (p0) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.0861 time to fit residues: 30.4303 Evaluate side-chains 152 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 120 optimal weight: 0.5980 chunk 155 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 HIS B 331 HIS C 266 ASN D 331 HIS E 331 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.114067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.084516 restraints weight = 37607.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.086741 restraints weight = 23275.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.088191 restraints weight = 17098.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.089035 restraints weight = 14061.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.089704 restraints weight = 12511.069| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13990 Z= 0.112 Angle : 0.604 6.886 18995 Z= 0.315 Chirality : 0.047 0.267 2125 Planarity : 0.004 0.044 2360 Dihedral : 5.711 24.464 1790 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.07 % Allowed : 0.33 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.20), residues: 1600 helix: 1.12 (0.26), residues: 380 sheet: -1.32 (0.21), residues: 455 loop : -0.91 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 317 TYR 0.016 0.001 TYR A 200 PHE 0.019 0.001 PHE B 324 TRP 0.020 0.002 TRP D 232 HIS 0.002 0.000 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00240 (13980) covalent geometry : angle 0.60411 (18975) SS BOND : bond 0.00220 ( 10) SS BOND : angle 0.43825 ( 20) hydrogen bonds : bond 0.04070 ( 500) hydrogen bonds : angle 4.31223 ( 1425) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.8396 (t0) cc_final: 0.7965 (p0) REVERT: B 94 THR cc_start: 0.9321 (t) cc_final: 0.8981 (t) REVERT: B 128 ASP cc_start: 0.8332 (t0) cc_final: 0.7831 (p0) REVERT: B 133 MET cc_start: 0.7558 (mtm) cc_final: 0.7110 (mtt) REVERT: C 38 ASP cc_start: 0.8594 (t0) cc_final: 0.8389 (t70) REVERT: C 94 THR cc_start: 0.9321 (t) cc_final: 0.9030 (t) REVERT: C 128 ASP cc_start: 0.8331 (t0) cc_final: 0.7773 (p0) REVERT: D 94 THR cc_start: 0.9317 (t) cc_final: 0.8982 (t) REVERT: D 128 ASP cc_start: 0.8390 (t0) cc_final: 0.7758 (p0) REVERT: D 176 MET cc_start: 0.9055 (ttm) cc_final: 0.8827 (ttp) REVERT: E 128 ASP cc_start: 0.8222 (t0) cc_final: 0.7924 (p0) REVERT: E 133 MET cc_start: 0.7319 (mtm) cc_final: 0.6802 (mtt) REVERT: E 225 ILE cc_start: 0.9518 (pt) cc_final: 0.9291 (pt) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.0915 time to fit residues: 31.6353 Evaluate side-chains 161 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 148 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 130 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 331 HIS E 331 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.111915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.081830 restraints weight = 40895.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.084125 restraints weight = 24066.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.085852 restraints weight = 17397.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.086691 restraints weight = 14086.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.087462 restraints weight = 12476.084| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13990 Z= 0.206 Angle : 0.681 6.655 18995 Z= 0.356 Chirality : 0.047 0.161 2125 Planarity : 0.004 0.070 2360 Dihedral : 5.927 25.292 1790 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.07 % Allowed : 0.78 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.20), residues: 1600 helix: 1.24 (0.27), residues: 380 sheet: -1.57 (0.21), residues: 455 loop : -1.00 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 317 TYR 0.021 0.002 TYR A 200 PHE 0.020 0.002 PHE C 324 TRP 0.023 0.001 TRP E 60 HIS 0.010 0.001 HIS D 331 Details of bonding type rmsd covalent geometry : bond 0.00472 (13980) covalent geometry : angle 0.68115 (18975) SS BOND : bond 0.00159 ( 10) SS BOND : angle 0.66257 ( 20) hydrogen bonds : bond 0.04852 ( 500) hydrogen bonds : angle 4.51463 ( 1425) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.8518 (t0) cc_final: 0.7911 (p0) REVERT: A 232 TRP cc_start: 0.8344 (t60) cc_final: 0.8091 (t60) REVERT: B 128 ASP cc_start: 0.8473 (t0) cc_final: 0.7853 (p0) REVERT: B 133 MET cc_start: 0.7887 (mtm) cc_final: 0.7562 (mtt) REVERT: C 128 ASP cc_start: 0.8446 (t0) cc_final: 0.7808 (p0) REVERT: D 128 ASP cc_start: 0.8520 (t0) cc_final: 0.7861 (p0) REVERT: D 133 MET cc_start: 0.7641 (mtm) cc_final: 0.7158 (mtt) REVERT: D 232 TRP cc_start: 0.8456 (t60) cc_final: 0.8201 (t60) REVERT: E 128 ASP cc_start: 0.8430 (t0) cc_final: 0.8016 (p0) REVERT: E 232 TRP cc_start: 0.8228 (t60) cc_final: 0.7093 (t60) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.0833 time to fit residues: 27.7173 Evaluate side-chains 152 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 34 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 331 HIS E 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.109770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.079855 restraints weight = 40642.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.082134 restraints weight = 24311.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.083709 restraints weight = 17592.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.084700 restraints weight = 14278.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.085229 restraints weight = 12562.847| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13990 Z= 0.175 Angle : 0.658 7.022 18995 Z= 0.345 Chirality : 0.047 0.347 2125 Planarity : 0.004 0.097 2360 Dihedral : 5.905 25.428 1790 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.20), residues: 1600 helix: 1.25 (0.27), residues: 380 sheet: -1.52 (0.21), residues: 450 loop : -1.06 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 317 TYR 0.018 0.001 TYR D 200 PHE 0.023 0.001 PHE A 324 TRP 0.017 0.001 TRP A 232 HIS 0.004 0.001 HIS E 331 Details of bonding type rmsd covalent geometry : bond 0.00407 (13980) covalent geometry : angle 0.65856 (18975) SS BOND : bond 0.00163 ( 10) SS BOND : angle 0.47758 ( 20) hydrogen bonds : bond 0.04800 ( 500) hydrogen bonds : angle 4.52269 ( 1425) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.8563 (t0) cc_final: 0.7881 (p0) REVERT: A 176 MET cc_start: 0.8759 (ttm) cc_final: 0.8398 (mtp) REVERT: A 232 TRP cc_start: 0.8181 (t60) cc_final: 0.7936 (t60) REVERT: B 94 THR cc_start: 0.9396 (t) cc_final: 0.8929 (t) REVERT: B 128 ASP cc_start: 0.8494 (t0) cc_final: 0.7782 (p0) REVERT: B 133 MET cc_start: 0.7737 (mtm) cc_final: 0.7504 (mtt) REVERT: B 176 MET cc_start: 0.8976 (ttp) cc_final: 0.8767 (ttm) REVERT: B 288 PHE cc_start: 0.8956 (t80) cc_final: 0.8744 (t80) REVERT: C 94 THR cc_start: 0.9403 (t) cc_final: 0.8976 (t) REVERT: C 128 ASP cc_start: 0.8482 (t0) cc_final: 0.7750 (p0) REVERT: C 133 MET cc_start: 0.7576 (mtm) cc_final: 0.6804 (mtt) REVERT: D 94 THR cc_start: 0.9363 (t) cc_final: 0.8911 (t) REVERT: D 128 ASP cc_start: 0.8530 (t0) cc_final: 0.7750 (p0) REVERT: D 232 TRP cc_start: 0.8458 (t60) cc_final: 0.8248 (t60) REVERT: E 128 ASP cc_start: 0.8470 (t0) cc_final: 0.7920 (p0) REVERT: E 176 MET cc_start: 0.8963 (ttp) cc_final: 0.8695 (ttp) REVERT: E 232 TRP cc_start: 0.8345 (t60) cc_final: 0.7530 (t60) REVERT: E 288 PHE cc_start: 0.8854 (t80) cc_final: 0.8456 (t80) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.0880 time to fit residues: 28.4279 Evaluate side-chains 148 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 28 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 24 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.110566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.080030 restraints weight = 39893.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.082400 restraints weight = 24013.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.083983 restraints weight = 17337.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.084897 restraints weight = 14059.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.085583 restraints weight = 12401.735| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 13990 Z= 0.149 Angle : 0.656 10.770 18995 Z= 0.338 Chirality : 0.046 0.165 2125 Planarity : 0.005 0.094 2360 Dihedral : 5.778 24.930 1790 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.20), residues: 1600 helix: 1.19 (0.27), residues: 380 sheet: -1.44 (0.21), residues: 450 loop : -0.99 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 317 TYR 0.016 0.001 TYR D 200 PHE 0.024 0.001 PHE E 324 TRP 0.014 0.001 TRP A 232 HIS 0.004 0.001 HIS E 331 Details of bonding type rmsd covalent geometry : bond 0.00344 (13980) covalent geometry : angle 0.65615 (18975) SS BOND : bond 0.00216 ( 10) SS BOND : angle 0.44522 ( 20) hydrogen bonds : bond 0.04410 ( 500) hydrogen bonds : angle 4.51730 ( 1425) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.8530 (t0) cc_final: 0.7959 (p0) REVERT: A 176 MET cc_start: 0.8714 (ttm) cc_final: 0.8388 (mtp) REVERT: A 232 TRP cc_start: 0.8145 (t60) cc_final: 0.7863 (t60) REVERT: B 94 THR cc_start: 0.9345 (t) cc_final: 0.8900 (t) REVERT: B 128 ASP cc_start: 0.8454 (t0) cc_final: 0.7818 (p0) REVERT: B 133 MET cc_start: 0.7680 (mtm) cc_final: 0.7405 (mtt) REVERT: B 176 MET cc_start: 0.8959 (ttp) cc_final: 0.8730 (ttm) REVERT: B 288 PHE cc_start: 0.8968 (t80) cc_final: 0.8725 (t80) REVERT: C 94 THR cc_start: 0.9389 (t) cc_final: 0.9026 (t) REVERT: C 128 ASP cc_start: 0.8443 (t0) cc_final: 0.7777 (p0) REVERT: D 94 THR cc_start: 0.9346 (t) cc_final: 0.8913 (t) REVERT: D 128 ASP cc_start: 0.8490 (t0) cc_final: 0.7845 (p0) REVERT: D 176 MET cc_start: 0.9079 (ttm) cc_final: 0.8857 (ttp) REVERT: D 232 TRP cc_start: 0.8470 (t60) cc_final: 0.8139 (t60) REVERT: E 128 ASP cc_start: 0.8413 (t0) cc_final: 0.7933 (p0) REVERT: E 176 MET cc_start: 0.8918 (ttp) cc_final: 0.8664 (ttp) REVERT: E 232 TRP cc_start: 0.8318 (t60) cc_final: 0.7395 (t60) REVERT: E 288 PHE cc_start: 0.8861 (t80) cc_final: 0.8478 (t80) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.0867 time to fit residues: 28.6315 Evaluate side-chains 145 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 158 optimal weight: 40.0000 chunk 53 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 90 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.110994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.080993 restraints weight = 39657.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.083320 restraints weight = 23577.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.084907 restraints weight = 16956.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.085748 restraints weight = 13764.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.086494 restraints weight = 12205.038| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13990 Z= 0.145 Angle : 0.651 8.940 18995 Z= 0.339 Chirality : 0.047 0.234 2125 Planarity : 0.004 0.083 2360 Dihedral : 5.760 24.495 1790 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.20), residues: 1600 helix: 1.19 (0.26), residues: 380 sheet: -1.37 (0.22), residues: 450 loop : -0.97 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 317 TYR 0.015 0.001 TYR B 200 PHE 0.025 0.001 PHE A 226 TRP 0.013 0.001 TRP D 232 HIS 0.004 0.001 HIS E 331 Details of bonding type rmsd covalent geometry : bond 0.00332 (13980) covalent geometry : angle 0.65052 (18975) SS BOND : bond 0.00278 ( 10) SS BOND : angle 0.65574 ( 20) hydrogen bonds : bond 0.04391 ( 500) hydrogen bonds : angle 4.48868 ( 1425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2056.07 seconds wall clock time: 36 minutes 21.70 seconds (2181.70 seconds total)