Starting phenix.real_space_refine on Sat Sep 12 04:09:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vxz_21453/09_2026/6vxz_21453.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxz_21453/09_2026/6vxz_21453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vxz_21453/09_2026/6vxz_21453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxz_21453/09_2026/6vxz_21453.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6vxz_21453/09_2026/6vxz_21453.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vxz_21453/09_2026/6vxz_21453.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vxz_21453/09_2026/6vxz_21453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxz_21453/09_2026/6vxz_21453.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 28 5.16 5 C 8876 2.51 5 N 2076 2.21 5 O 2332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13324 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3091 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 1 Chain: "A" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 240 Unusual residues: {'PGW': 6} Classifications: {'RNAv2': 1, 'undetermined': 6} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PGW:plan-3': 2} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: B, C, D Time building chain proxies: 2.71, per 1000 atoms: 0.20 Number of scatterers: 13324 At special positions: 0 Unit cell: (101.937, 101.937, 118.379, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 12 15.00 O 2332 8.00 N 2076 7.00 C 8876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 548.7 milliseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2952 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 8 sheets defined 67.4% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 10 through 36 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 43 through 62 removed outlier: 4.071A pdb=" N ASP A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 3.527A pdb=" N LEU A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.619A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 98 Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.911A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 113 through 126 removed outlier: 4.155A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 156 Processing helix chain 'A' and resid 165 through 182 removed outlier: 3.526A pdb=" N TYR A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 223 removed outlier: 3.838A pdb=" N LEU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 214 " --> pdb=" O MET A 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 215 " --> pdb=" O TYR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 246 removed outlier: 4.072A pdb=" N ARG A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 246 " --> pdb=" O PHE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 removed outlier: 3.583A pdb=" N GLN A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 307 through 315 removed outlier: 5.374A pdb=" N ARG A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 395 through 403 removed outlier: 3.525A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 removed outlier: 4.061A pdb=" N GLN A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 36 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 43 through 62 removed outlier: 4.071A pdb=" N ASP B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Proline residue: B 59 - end of helix removed outlier: 3.527A pdb=" N LEU B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.619A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 98 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.912A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 113 through 126 removed outlier: 4.155A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 156 Processing helix chain 'B' and resid 165 through 182 removed outlier: 3.526A pdb=" N TYR B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 223 removed outlier: 3.838A pdb=" N LEU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE B 215 " --> pdb=" O TYR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 246 removed outlier: 4.073A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 268 removed outlier: 3.583A pdb=" N GLN B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 292 through 297 Processing helix chain 'B' and resid 307 through 315 removed outlier: 5.374A pdb=" N ARG B 311 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 Processing helix chain 'B' and resid 395 through 403 removed outlier: 3.525A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 removed outlier: 4.061A pdb=" N GLN B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 36 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 43 through 62 removed outlier: 4.071A pdb=" N ASP C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.528A pdb=" N LEU C 62 " --> pdb=" O ILE C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.619A pdb=" N LEU C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 101 through 106 removed outlier: 3.911A pdb=" N LEU C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 113 through 126 removed outlier: 4.155A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 156 Processing helix chain 'C' and resid 165 through 182 removed outlier: 3.527A pdb=" N TYR C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 171 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 223 removed outlier: 3.838A pdb=" N LEU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL C 214 " --> pdb=" O MET C 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE C 215 " --> pdb=" O TYR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 246 removed outlier: 4.073A pdb=" N ARG C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 246 " --> pdb=" O PHE C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 268 removed outlier: 3.583A pdb=" N GLN C 253 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 292 through 297 Processing helix chain 'C' and resid 307 through 315 removed outlier: 5.374A pdb=" N ARG C 311 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 395 through 403 removed outlier: 3.526A pdb=" N SER C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 removed outlier: 4.061A pdb=" N GLN C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 36 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 43 through 62 removed outlier: 4.071A pdb=" N ASP D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Proline residue: D 59 - end of helix removed outlier: 3.527A pdb=" N LEU D 62 " --> pdb=" O ILE D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.620A pdb=" N LEU D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 98 Processing helix chain 'D' and resid 101 through 106 removed outlier: 3.911A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 112 Processing helix chain 'D' and resid 113 through 126 removed outlier: 4.155A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 156 Processing helix chain 'D' and resid 165 through 182 removed outlier: 3.526A pdb=" N TYR D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 223 removed outlier: 3.838A pdb=" N LEU D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL D 214 " --> pdb=" O MET D 210 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 215 " --> pdb=" O TYR D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 246 removed outlier: 4.073A pdb=" N ARG D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS D 246 " --> pdb=" O PHE D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 268 removed outlier: 3.583A pdb=" N GLN D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 292 through 297 Processing helix chain 'D' and resid 307 through 315 removed outlier: 5.374A pdb=" N ARG D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 395 through 403 removed outlier: 3.526A pdb=" N SER D 402 " --> pdb=" O ASP D 398 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 412 removed outlier: 4.061A pdb=" N GLN D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 319 removed outlier: 3.668A pdb=" N VAL A 338 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 7.027A pdb=" N TYR A 327 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA A 383 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 329 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 319 removed outlier: 3.669A pdb=" N VAL B 338 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 7.027A pdb=" N TYR B 327 " --> pdb=" O ALA B 383 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA B 383 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE B 329 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 319 removed outlier: 3.669A pdb=" N VAL C 338 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 7.028A pdb=" N TYR C 327 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA C 383 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 329 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 319 removed outlier: 3.668A pdb=" N VAL D 338 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 7.027A pdb=" N TYR D 327 " --> pdb=" O ALA D 383 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA D 383 " --> pdb=" O TYR D 327 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE D 329 " --> pdb=" O VAL D 381 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1956 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: 2.03 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2108 1.32 - 1.44: 3371 1.44 - 1.57: 8045 1.57 - 1.69: 20 1.69 - 1.81: 52 Bond restraints: 13596 Sorted by residual: bond pdb=" C5 CMP B 501 " pdb=" C6 CMP B 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C5 CMP A 501 " pdb=" C6 CMP A 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C5 CMP D 501 " pdb=" C6 CMP D 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C8 CMP D 501 " pdb=" N9 CMP D 501 " ideal model delta sigma weight residual 1.337 1.422 -0.085 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C8 CMP C 501 " pdb=" N9 CMP C 501 " ideal model delta sigma weight residual 1.337 1.422 -0.085 2.00e-02 2.50e+03 1.81e+01 ... (remaining 13591 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 17209 2.10 - 4.21: 870 4.21 - 6.31: 171 6.31 - 8.42: 30 8.42 - 10.52: 24 Bond angle restraints: 18304 Sorted by residual: angle pdb=" N GLU D 395 " pdb=" CA GLU D 395 " pdb=" C GLU D 395 " ideal model delta sigma weight residual 111.14 105.04 6.10 1.08e+00 8.57e-01 3.19e+01 angle pdb=" N GLU C 395 " pdb=" CA GLU C 395 " pdb=" C GLU C 395 " ideal model delta sigma weight residual 111.14 105.04 6.10 1.08e+00 8.57e-01 3.19e+01 angle pdb=" N GLU A 395 " pdb=" CA GLU A 395 " pdb=" C GLU A 395 " ideal model delta sigma weight residual 111.14 105.06 6.08 1.08e+00 8.57e-01 3.17e+01 angle pdb=" N GLU B 395 " pdb=" CA GLU B 395 " pdb=" C GLU B 395 " ideal model delta sigma weight residual 111.14 105.09 6.05 1.08e+00 8.57e-01 3.14e+01 angle pdb=" C ASP B 393 " pdb=" N LYS B 394 " pdb=" CA LYS B 394 " ideal model delta sigma weight residual 121.54 132.01 -10.47 1.91e+00 2.74e-01 3.01e+01 ... (remaining 18299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.77: 7600 27.77 - 55.53: 568 55.53 - 83.30: 84 83.30 - 111.07: 24 111.07 - 138.84: 4 Dihedral angle restraints: 8280 sinusoidal: 3704 harmonic: 4576 Sorted by residual: dihedral pdb=" C5' CMP D 501 " pdb=" O5' CMP D 501 " pdb=" P CMP D 501 " pdb=" O1P CMP D 501 " ideal model delta sinusoidal sigma weight residual 60.00 168.08 -108.08 1 2.00e+01 2.50e-03 3.15e+01 dihedral pdb=" C5' CMP B 501 " pdb=" O5' CMP B 501 " pdb=" P CMP B 501 " pdb=" O1P CMP B 501 " ideal model delta sinusoidal sigma weight residual 60.00 168.07 -108.07 1 2.00e+01 2.50e-03 3.14e+01 dihedral pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual 60.00 168.04 -108.04 1 2.00e+01 2.50e-03 3.14e+01 ... (remaining 8277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1609 0.063 - 0.126: 412 0.126 - 0.188: 49 0.188 - 0.251: 18 0.251 - 0.314: 4 Chirality restraints: 2092 Sorted by residual: chirality pdb=" CA ALA B 408 " pdb=" N ALA B 408 " pdb=" C ALA B 408 " pdb=" CB ALA B 408 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ALA A 408 " pdb=" N ALA A 408 " pdb=" C ALA A 408 " pdb=" CB ALA A 408 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CA ALA C 408 " pdb=" N ALA C 408 " pdb=" C ALA C 408 " pdb=" CB ALA C 408 " both_signs ideal model delta sigma weight residual False 2.48 2.17 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 2089 not shown) Planarity restraints: 2196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 502 " 0.076 2.00e-02 2.50e+03 1.50e-01 2.26e+02 pdb=" C10 PGW A 502 " -0.199 2.00e-02 2.50e+03 pdb=" C8 PGW A 502 " -0.076 2.00e-02 2.50e+03 pdb=" C9 PGW A 502 " 0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW B 502 " -0.076 2.00e-02 2.50e+03 1.50e-01 2.26e+02 pdb=" C10 PGW B 502 " 0.198 2.00e-02 2.50e+03 pdb=" C8 PGW B 502 " 0.076 2.00e-02 2.50e+03 pdb=" C9 PGW B 502 " -0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 502 " 0.076 2.00e-02 2.50e+03 1.50e-01 2.26e+02 pdb=" C10 PGW D 502 " -0.198 2.00e-02 2.50e+03 pdb=" C8 PGW D 502 " -0.076 2.00e-02 2.50e+03 pdb=" C9 PGW D 502 " 0.198 2.00e-02 2.50e+03 ... (remaining 2193 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 100 2.55 - 3.14: 10756 3.14 - 3.72: 18817 3.72 - 4.31: 26624 4.31 - 4.90: 45936 Nonbonded interactions: 102233 Sorted by model distance: nonbonded pdb=" O THR A 182 " pdb=" OG1 THR A 183 " model vdw 1.959 3.040 nonbonded pdb=" O THR D 182 " pdb=" OG1 THR D 183 " model vdw 1.959 3.040 nonbonded pdb=" O THR C 182 " pdb=" OG1 THR C 183 " model vdw 1.959 3.040 nonbonded pdb=" O THR B 182 " pdb=" OG1 THR B 183 " model vdw 1.959 3.040 nonbonded pdb=" ND1 HIS A 149 " pdb=" OH TYR A 170 " model vdw 2.260 3.120 ... (remaining 102228 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.970 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.086 13596 Z= 0.504 Angle : 1.095 10.523 18304 Z= 0.566 Chirality : 0.058 0.314 2092 Planarity : 0.008 0.150 2196 Dihedral : 19.622 138.837 5328 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.40 % Allowed : 17.72 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.19), residues: 1540 helix: -2.12 (0.14), residues: 1032 sheet: -3.22 (0.43), residues: 120 loop : -3.24 (0.26), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 399 TYR 0.014 0.001 TYR D 175 PHE 0.011 0.001 PHE A 397 TRP 0.006 0.002 TRP B 18 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.01109 / 0.50 (13596) covalent geometry : angle 1.09451 / 0.57 (18304) hydrogen bonds : bond 0.14080 / 9.13 ( 680) hydrogen bonds : angle 7.02920 / 5.13 ( 1956) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 301 LEU cc_start: 0.4769 (OUTLIER) cc_final: 0.4314 (pt) REVERT: A 393 ASP cc_start: 0.6847 (OUTLIER) cc_final: 0.6186 (t0) REVERT: B 301 LEU cc_start: 0.4761 (OUTLIER) cc_final: 0.4302 (pt) REVERT: B 393 ASP cc_start: 0.7024 (OUTLIER) cc_final: 0.6223 (t0) REVERT: C 301 LEU cc_start: 0.4806 (OUTLIER) cc_final: 0.4340 (pt) REVERT: C 329 ILE cc_start: 0.9037 (mt) cc_final: 0.8835 (mt) REVERT: C 393 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6229 (t0) REVERT: D 301 LEU cc_start: 0.4770 (OUTLIER) cc_final: 0.4306 (pt) REVERT: D 393 ASP cc_start: 0.6854 (OUTLIER) cc_final: 0.6196 (t0) outliers start: 32 outliers final: 13 residues processed: 178 average time/residue: 0.1140 time to fit residues: 29.3392 Evaluate side-chains 125 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 393 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.162370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127774 restraints weight = 15366.467| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.16 r_work: 0.3039 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13596 Z= 0.140 Angle : 0.714 9.132 18304 Z= 0.323 Chirality : 0.044 0.194 2092 Planarity : 0.005 0.047 2196 Dihedral : 18.015 121.610 2442 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.15 % Allowed : 18.99 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.22), residues: 1540 helix: -0.17 (0.17), residues: 1008 sheet: -1.91 (0.47), residues: 112 loop : -2.65 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 382 TYR 0.012 0.001 TYR A 25 PHE 0.005 0.001 PHE B 40 TRP 0.003 0.001 TRP A 155 HIS 0.002 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (13596) covalent geometry : angle 0.71394 / 0.32 (18304) hydrogen bonds : bond 0.03699 / 2.43 ( 680) hydrogen bonds : angle 4.51887 / 3.24 ( 1956) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 0.439 Fit side-chains REVERT: A 224 LYS cc_start: 0.8979 (mttp) cc_final: 0.8763 (mttm) REVERT: A 329 ILE cc_start: 0.8889 (mt) cc_final: 0.8674 (mt) REVERT: B 224 LYS cc_start: 0.8975 (mttp) cc_final: 0.8754 (mttm) REVERT: B 329 ILE cc_start: 0.8882 (mt) cc_final: 0.8668 (mt) REVERT: C 224 LYS cc_start: 0.8981 (mttp) cc_final: 0.8771 (mttm) REVERT: D 224 LYS cc_start: 0.8984 (mttp) cc_final: 0.8770 (mttm) REVERT: D 329 ILE cc_start: 0.8877 (mt) cc_final: 0.8666 (mt) outliers start: 42 outliers final: 11 residues processed: 159 average time/residue: 0.1285 time to fit residues: 28.7589 Evaluate side-chains 118 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 295 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 127 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 144 optimal weight: 0.0470 chunk 2 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.161489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.124891 restraints weight = 15671.191| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.28 r_work: 0.3012 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13596 Z= 0.116 Angle : 0.669 9.091 18304 Z= 0.300 Chirality : 0.042 0.204 2092 Planarity : 0.004 0.054 2196 Dihedral : 15.722 91.387 2396 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.18 % Allowed : 20.87 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.22), residues: 1540 helix: 0.50 (0.18), residues: 1004 sheet: -1.81 (0.44), residues: 116 loop : -2.06 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 111 TYR 0.009 0.001 TYR A 175 PHE 0.005 0.001 PHE D 397 TRP 0.003 0.001 TRP D 155 HIS 0.002 0.000 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13596) covalent geometry : angle 0.66924 / 0.30 (18304) hydrogen bonds : bond 0.03295 / 2.16 ( 680) hydrogen bonds : angle 3.95796 / 2.84 ( 1956) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.477 Fit side-chains REVERT: A 224 LYS cc_start: 0.9039 (mttp) cc_final: 0.8838 (mttm) REVERT: C 373 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6254 (mt) REVERT: D 224 LYS cc_start: 0.9033 (mttp) cc_final: 0.8833 (mttm) outliers start: 29 outliers final: 7 residues processed: 147 average time/residue: 0.1311 time to fit residues: 27.2774 Evaluate side-chains 112 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 124 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 17 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.0970 chunk 145 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.161248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.124100 restraints weight = 15669.792| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.34 r_work: 0.2991 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13596 Z= 0.108 Angle : 0.650 9.517 18304 Z= 0.289 Chirality : 0.041 0.183 2092 Planarity : 0.005 0.063 2196 Dihedral : 14.312 89.839 2396 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.25 % Allowed : 20.87 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.23), residues: 1540 helix: 0.84 (0.18), residues: 1012 sheet: -1.44 (0.48), residues: 96 loop : -1.49 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 311 TYR 0.010 0.001 TYR C 175 PHE 0.006 0.001 PHE A 36 TRP 0.004 0.001 TRP D 176 HIS 0.001 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (13596) covalent geometry : angle 0.65032 / 0.29 (18304) hydrogen bonds : bond 0.03131 / 2.05 ( 680) hydrogen bonds : angle 3.69328 / 2.64 ( 1956) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.488 Fit side-chains REVERT: A 22 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7910 (t) REVERT: A 230 LEU cc_start: 0.8665 (mm) cc_final: 0.8460 (mt) REVERT: A 373 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.6129 (mt) REVERT: B 230 LEU cc_start: 0.8655 (mm) cc_final: 0.8450 (mt) REVERT: B 362 GLU cc_start: 0.8157 (pt0) cc_final: 0.7791 (mt-10) REVERT: B 373 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6123 (mt) REVERT: C 362 GLU cc_start: 0.8147 (pt0) cc_final: 0.7785 (mt-10) REVERT: C 373 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6163 (mt) REVERT: D 362 GLU cc_start: 0.8139 (pt0) cc_final: 0.7782 (mt-10) REVERT: D 373 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.6142 (mt) outliers start: 30 outliers final: 17 residues processed: 153 average time/residue: 0.1067 time to fit residues: 24.0618 Evaluate side-chains 131 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 72 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.151341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.112163 restraints weight = 16052.220| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.56 r_work: 0.2825 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13596 Z= 0.195 Angle : 0.722 8.601 18304 Z= 0.331 Chirality : 0.045 0.189 2092 Planarity : 0.005 0.058 2196 Dihedral : 14.729 87.847 2396 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.05 % Allowed : 20.57 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.22), residues: 1540 helix: 0.74 (0.18), residues: 1004 sheet: -1.40 (0.44), residues: 116 loop : -1.49 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 233 TYR 0.014 0.001 TYR B 175 PHE 0.007 0.001 PHE B 365 TRP 0.008 0.001 TRP D 155 HIS 0.003 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.19 (13596) covalent geometry : angle 0.72228 / 0.33 (18304) hydrogen bonds : bond 0.04108 / 2.69 ( 680) hydrogen bonds : angle 3.83384 / 2.75 ( 1956) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 112 time to evaluate : 0.454 Fit side-chains REVERT: A 22 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.8040 (t) REVERT: A 230 LEU cc_start: 0.8957 (mm) cc_final: 0.8634 (mt) REVERT: A 362 GLU cc_start: 0.8286 (pt0) cc_final: 0.7931 (mt-10) REVERT: A 373 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6142 (mt) REVERT: B 230 LEU cc_start: 0.8944 (mm) cc_final: 0.8625 (mt) REVERT: B 362 GLU cc_start: 0.8291 (pt0) cc_final: 0.7939 (mt-10) REVERT: B 373 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6140 (mt) REVERT: C 362 GLU cc_start: 0.8295 (pt0) cc_final: 0.7942 (mt-10) REVERT: D 362 GLU cc_start: 0.8283 (pt0) cc_final: 0.7933 (mt-10) REVERT: D 373 LEU cc_start: 0.6582 (OUTLIER) cc_final: 0.6146 (mt) outliers start: 54 outliers final: 28 residues processed: 160 average time/residue: 0.1042 time to fit residues: 25.2831 Evaluate side-chains 136 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 29 optimal weight: 0.1980 chunk 32 optimal weight: 6.9990 chunk 139 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 138 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.155366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116923 restraints weight = 16010.441| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.42 r_work: 0.2910 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13596 Z= 0.131 Angle : 0.665 9.546 18304 Z= 0.299 Chirality : 0.042 0.164 2092 Planarity : 0.005 0.055 2196 Dihedral : 13.738 84.468 2396 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.05 % Allowed : 20.42 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.23), residues: 1540 helix: 0.90 (0.18), residues: 1004 sheet: -1.36 (0.45), residues: 116 loop : -1.22 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 311 TYR 0.010 0.001 TYR D 175 PHE 0.007 0.001 PHE D 36 TRP 0.003 0.001 TRP C 176 HIS 0.002 0.000 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (13596) covalent geometry : angle 0.66461 / 0.30 (18304) hydrogen bonds : bond 0.03460 / 2.26 ( 680) hydrogen bonds : angle 3.67089 / 2.62 ( 1956) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 111 time to evaluate : 0.325 Fit side-chains REVERT: A 22 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7965 (t) REVERT: A 230 LEU cc_start: 0.8904 (mm) cc_final: 0.8667 (mt) REVERT: A 362 GLU cc_start: 0.8191 (pt0) cc_final: 0.7842 (mt-10) REVERT: A 369 MET cc_start: 0.8213 (mmt) cc_final: 0.7866 (mtt) REVERT: A 373 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.6076 (mt) REVERT: B 57 ASP cc_start: 0.6844 (t70) cc_final: 0.6599 (t70) REVERT: B 230 LEU cc_start: 0.8881 (mm) cc_final: 0.8646 (mt) REVERT: B 362 GLU cc_start: 0.8187 (pt0) cc_final: 0.7849 (mt-10) REVERT: B 369 MET cc_start: 0.8203 (mmt) cc_final: 0.7891 (mtt) REVERT: B 373 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6092 (mt) REVERT: C 362 GLU cc_start: 0.8195 (pt0) cc_final: 0.7858 (mt-10) REVERT: C 373 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6072 (mt) REVERT: D 362 GLU cc_start: 0.8189 (pt0) cc_final: 0.7845 (mt-10) REVERT: D 369 MET cc_start: 0.8214 (mmt) cc_final: 0.7877 (mtt) REVERT: D 373 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6060 (mt) outliers start: 54 outliers final: 33 residues processed: 161 average time/residue: 0.1036 time to fit residues: 24.9183 Evaluate side-chains 140 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 2 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 0.0770 chunk 107 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.152418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.112986 restraints weight = 16014.107| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.53 r_work: 0.2832 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13596 Z= 0.150 Angle : 0.685 9.042 18304 Z= 0.309 Chirality : 0.043 0.165 2092 Planarity : 0.005 0.057 2196 Dihedral : 13.524 76.665 2396 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.20 % Allowed : 20.57 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1540 helix: 0.93 (0.18), residues: 996 sheet: -1.28 (0.46), residues: 116 loop : -0.91 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 111 TYR 0.012 0.001 TYR C 175 PHE 0.007 0.001 PHE D 36 TRP 0.005 0.001 TRP A 155 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (13596) covalent geometry : angle 0.68451 / 0.31 (18304) hydrogen bonds : bond 0.03651 / 2.39 ( 680) hydrogen bonds : angle 3.65642 / 2.62 ( 1956) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 115 time to evaluate : 0.403 Fit side-chains REVERT: A 22 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8070 (t) REVERT: A 230 LEU cc_start: 0.8981 (mm) cc_final: 0.8671 (mt) REVERT: A 362 GLU cc_start: 0.8265 (pt0) cc_final: 0.7870 (mt-10) REVERT: A 369 MET cc_start: 0.8221 (mmt) cc_final: 0.7855 (mtt) REVERT: A 373 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6073 (mt) REVERT: B 230 LEU cc_start: 0.8950 (mm) cc_final: 0.8719 (mt) REVERT: B 362 GLU cc_start: 0.8288 (pt0) cc_final: 0.7887 (mt-10) REVERT: B 369 MET cc_start: 0.8246 (mmt) cc_final: 0.7886 (mtt) REVERT: B 373 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6075 (mt) REVERT: C 362 GLU cc_start: 0.8284 (pt0) cc_final: 0.7869 (mt-10) REVERT: C 373 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6107 (mt) REVERT: D 362 GLU cc_start: 0.8282 (pt0) cc_final: 0.7879 (mt-10) REVERT: D 369 MET cc_start: 0.8238 (mmt) cc_final: 0.7874 (mtt) REVERT: D 373 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6075 (mt) outliers start: 56 outliers final: 35 residues processed: 166 average time/residue: 0.0968 time to fit residues: 24.4396 Evaluate side-chains 146 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 92 optimal weight: 0.0470 chunk 98 optimal weight: 0.0070 chunk 106 optimal weight: 0.0010 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.156630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.117086 restraints weight = 15725.539| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.34 r_work: 0.2904 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13596 Z= 0.104 Angle : 0.655 9.635 18304 Z= 0.290 Chirality : 0.041 0.156 2092 Planarity : 0.005 0.058 2196 Dihedral : 12.531 63.255 2396 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.55 % Allowed : 22.45 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.23), residues: 1540 helix: 1.12 (0.18), residues: 1012 sheet: -1.34 (0.51), residues: 96 loop : -0.78 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 377 TYR 0.009 0.001 TYR D 259 PHE 0.008 0.001 PHE D 36 TRP 0.003 0.000 TRP A 264 HIS 0.001 0.000 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (13596) covalent geometry : angle 0.65537 / 0.29 (18304) hydrogen bonds : bond 0.03044 / 1.99 ( 680) hydrogen bonds : angle 3.53040 / 2.52 ( 1956) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.8020 (t) REVERT: A 57 ASP cc_start: 0.6829 (t70) cc_final: 0.6572 (t70) REVERT: A 230 LEU cc_start: 0.8889 (mm) cc_final: 0.8670 (mt) REVERT: A 362 GLU cc_start: 0.8226 (pt0) cc_final: 0.7861 (mt-10) REVERT: A 369 MET cc_start: 0.8152 (mmt) cc_final: 0.7758 (mtt) REVERT: A 373 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6033 (mt) REVERT: B 57 ASP cc_start: 0.6830 (t70) cc_final: 0.6597 (t70) REVERT: B 230 LEU cc_start: 0.8860 (mm) cc_final: 0.8649 (mt) REVERT: B 362 GLU cc_start: 0.8245 (pt0) cc_final: 0.7860 (mt-10) REVERT: B 369 MET cc_start: 0.8136 (mmt) cc_final: 0.7760 (mtt) REVERT: B 373 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6030 (mt) REVERT: C 57 ASP cc_start: 0.6823 (t70) cc_final: 0.6573 (t70) REVERT: C 362 GLU cc_start: 0.8238 (pt0) cc_final: 0.7858 (mt-10) REVERT: C 369 MET cc_start: 0.8182 (mmt) cc_final: 0.7755 (mtt) REVERT: C 373 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6037 (mt) REVERT: D 57 ASP cc_start: 0.6818 (t70) cc_final: 0.6584 (t70) REVERT: D 362 GLU cc_start: 0.8247 (pt0) cc_final: 0.7872 (mt-10) REVERT: D 369 MET cc_start: 0.8164 (mmt) cc_final: 0.7772 (mtt) REVERT: D 373 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6032 (mt) outliers start: 34 outliers final: 15 residues processed: 165 average time/residue: 0.1099 time to fit residues: 26.3782 Evaluate side-chains 140 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 4 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 129 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 60 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.155892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.117028 restraints weight = 15907.138| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.37 r_work: 0.2891 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13596 Z= 0.109 Angle : 0.652 8.969 18304 Z= 0.290 Chirality : 0.041 0.160 2092 Planarity : 0.005 0.061 2196 Dihedral : 12.193 61.059 2396 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.80 % Allowed : 23.57 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.23), residues: 1540 helix: 1.21 (0.18), residues: 1012 sheet: -1.37 (0.52), residues: 96 loop : -0.64 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 377 TYR 0.009 0.001 TYR A 175 PHE 0.008 0.001 PHE B 36 TRP 0.003 0.001 TRP A 176 HIS 0.002 0.000 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (13596) covalent geometry : angle 0.65222 / 0.29 (18304) hydrogen bonds : bond 0.03147 / 2.06 ( 680) hydrogen bonds : angle 3.50186 / 2.50 ( 1956) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.480 Fit side-chains REVERT: A 57 ASP cc_start: 0.6861 (t70) cc_final: 0.6548 (t70) REVERT: A 230 LEU cc_start: 0.8874 (mm) cc_final: 0.8645 (mt) REVERT: A 362 GLU cc_start: 0.8258 (pt0) cc_final: 0.7862 (mt-10) REVERT: A 369 MET cc_start: 0.8115 (mmt) cc_final: 0.7760 (mtt) REVERT: A 373 LEU cc_start: 0.6411 (OUTLIER) cc_final: 0.6007 (mt) REVERT: B 57 ASP cc_start: 0.6979 (t70) cc_final: 0.6721 (t70) REVERT: B 230 LEU cc_start: 0.8854 (mm) cc_final: 0.8629 (mt) REVERT: B 362 GLU cc_start: 0.8274 (pt0) cc_final: 0.7875 (mt-10) REVERT: B 369 MET cc_start: 0.8133 (mmt) cc_final: 0.7761 (mtt) REVERT: B 373 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.5996 (mt) REVERT: C 57 ASP cc_start: 0.6961 (t70) cc_final: 0.6697 (t70) REVERT: C 362 GLU cc_start: 0.8266 (pt0) cc_final: 0.7856 (mt-10) REVERT: C 369 MET cc_start: 0.8161 (mmt) cc_final: 0.7811 (mtt) REVERT: C 373 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.5927 (mt) REVERT: D 57 ASP cc_start: 0.6959 (t70) cc_final: 0.6703 (t70) REVERT: D 362 GLU cc_start: 0.8274 (pt0) cc_final: 0.7871 (mt-10) REVERT: D 369 MET cc_start: 0.8107 (mmt) cc_final: 0.7749 (mtt) REVERT: D 373 LEU cc_start: 0.6408 (OUTLIER) cc_final: 0.6005 (mt) outliers start: 24 outliers final: 15 residues processed: 148 average time/residue: 0.1125 time to fit residues: 24.3927 Evaluate side-chains 137 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 64 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 20 optimal weight: 0.3980 chunk 142 optimal weight: 0.0670 chunk 105 optimal weight: 2.9990 chunk 139 optimal weight: 0.0040 chunk 146 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 75 optimal weight: 0.0770 chunk 111 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.2488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.158745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120819 restraints weight = 15709.359| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.28 r_work: 0.2965 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13596 Z= 0.102 Angle : 0.660 10.476 18304 Z= 0.290 Chirality : 0.041 0.148 2092 Planarity : 0.005 0.062 2196 Dihedral : 11.432 58.433 2396 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.73 % Allowed : 24.02 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.23), residues: 1540 helix: 1.41 (0.18), residues: 996 sheet: -0.76 (0.54), residues: 88 loop : -0.45 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 111 TYR 0.009 0.001 TYR C 259 PHE 0.009 0.001 PHE D 36 TRP 0.004 0.000 TRP B 264 HIS 0.001 0.000 HIS D 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (13596) covalent geometry : angle 0.65985 / 0.29 (18304) hydrogen bonds : bond 0.02881 / 1.89 ( 680) hydrogen bonds : angle 3.50920 / 2.51 ( 1956) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.402 Fit side-chains REVERT: A 57 ASP cc_start: 0.6909 (t70) cc_final: 0.6618 (t70) REVERT: A 230 LEU cc_start: 0.8769 (mm) cc_final: 0.8561 (mt) REVERT: A 362 GLU cc_start: 0.8213 (pt0) cc_final: 0.7836 (mt-10) REVERT: A 369 MET cc_start: 0.8157 (mmt) cc_final: 0.7749 (mtt) REVERT: A 373 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.5964 (mt) REVERT: B 57 ASP cc_start: 0.6852 (t70) cc_final: 0.6552 (t70) REVERT: B 230 LEU cc_start: 0.8768 (mm) cc_final: 0.8562 (mt) REVERT: B 362 GLU cc_start: 0.8240 (pt0) cc_final: 0.7840 (mt-10) REVERT: B 369 MET cc_start: 0.8016 (mmt) cc_final: 0.7635 (mtt) REVERT: B 373 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.5959 (mt) REVERT: C 57 ASP cc_start: 0.6875 (t70) cc_final: 0.6567 (t70) REVERT: C 362 GLU cc_start: 0.8239 (pt0) cc_final: 0.7833 (mt-10) REVERT: C 369 MET cc_start: 0.8116 (mmt) cc_final: 0.7705 (mtt) REVERT: C 373 LEU cc_start: 0.6291 (OUTLIER) cc_final: 0.5879 (mt) REVERT: D 57 ASP cc_start: 0.6847 (t70) cc_final: 0.6539 (t70) REVERT: D 362 GLU cc_start: 0.8239 (pt0) cc_final: 0.7840 (mt-10) REVERT: D 369 MET cc_start: 0.8072 (mmt) cc_final: 0.7654 (mtt) REVERT: D 373 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.5960 (mt) outliers start: 23 outliers final: 16 residues processed: 143 average time/residue: 0.1124 time to fit residues: 23.4635 Evaluate side-chains 136 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 90 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 54 optimal weight: 0.0980 chunk 22 optimal weight: 0.0970 chunk 94 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.157625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.121630 restraints weight = 15879.193| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.28 r_work: 0.2965 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13596 Z= 0.108 Angle : 0.656 9.763 18304 Z= 0.291 Chirality : 0.041 0.148 2092 Planarity : 0.005 0.062 2196 Dihedral : 11.307 56.574 2396 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.10 % Allowed : 23.80 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.23), residues: 1540 helix: 1.52 (0.18), residues: 996 sheet: -0.82 (0.54), residues: 88 loop : -0.38 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 311 TYR 0.009 0.001 TYR A 175 PHE 0.007 0.001 PHE D 36 TRP 0.003 0.001 TRP C 176 HIS 0.001 0.000 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (13596) covalent geometry : angle 0.65620 / 0.29 (18304) hydrogen bonds : bond 0.03017 / 1.97 ( 680) hydrogen bonds : angle 3.47209 / 2.48 ( 1956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2521.76 seconds wall clock time: 44 minutes 3.74 seconds (2643.74 seconds total)