Starting phenix.real_space_refine on Sat Aug 23 17:29:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vxz_21453/08_2025/6vxz_21453.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxz_21453/08_2025/6vxz_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_21453/08_2025/6vxz_21453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxz_21453/08_2025/6vxz_21453.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vxz_21453/08_2025/6vxz_21453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxz_21453/08_2025/6vxz_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: {'RNA': 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: 101 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: 1.94, per 1000 atoms: 0.15 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: 0.78 Conformation dependent library (CDL) restraints added in 498.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.33 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: 1.72 Time building geometry restraints manager: 1.04 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: 17222 2.10 - 4.21: 873 4.21 - 6.31: 171 6.31 - 8.42: 22 8.42 - 10.52: 16 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 - 34.43: 7872 34.43 - 68.85: 428 68.85 - 103.28: 56 103.28 - 137.70: 12 137.70 - 172.13: 32 Dihedral angle restraints: 8400 sinusoidal: 3824 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 8397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1613 0.063 - 0.126: 412 0.126 - 0.188: 49 0.188 - 0.251: 14 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: 0.980 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.470 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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= 0.503 Angle : 1.068 10.523 18304 Z= 0.563 Chirality : 0.057 0.314 2092 Planarity : 0.008 0.150 2196 Dihedral : 23.657 172.130 5448 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 aren 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 covalent geometry : bond 0.01107 (13596) covalent geometry : angle 1.06770 (18304) hydrogen bonds : bond 0.14080 ( 680) hydrogen bonds : angle 7.02920 ( 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 : 0.498 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: 0.8834 (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: 0.1259 time to fit residues: 32.2134 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 : 0.480 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.162569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128473 restraints weight = 15336.917| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.14 r_work: 0.3041 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13596 Z= 0.146 Angle : 0.685 9.183 18304 Z= 0.323 Chirality : 0.044 0.176 2092 Planarity : 0.005 0.047 2196 Dihedral : 25.405 164.607 2562 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.08 % Allowed : 18.62 % Favored : 78.30 % 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 aren not related in a simple way. whole: -1.57 (0.22), residues: 1540 helix: -0.19 (0.17), residues: 1008 sheet: -1.86 (0.46), residues: 120 loop : -2.69 (0.27), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 382 TYR 0.013 0.001 TYR A 25 PHE 0.005 0.001 PHE A 36 TRP 0.003 0.001 TRP A 155 HIS 0.002 0.001 HIS D 149 Details of bonding type rmsd covalent geometry : bond 0.00340 (13596) covalent geometry : angle 0.68548 (18304) hydrogen bonds : bond 0.03732 ( 680) hydrogen bonds : angle 4.55424 ( 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 160 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 0.527 Fit side-chains REVERT: A 224 LYS cc_start: 0.8976 (mttp) cc_final: 0.8753 (mttm) REVERT: A 329 ILE cc_start: 0.8882 (mt) cc_final: 0.8672 (mt) REVERT: B 224 LYS cc_start: 0.8971 (mttp) cc_final: 0.8749 (mttm) REVERT: B 329 ILE cc_start: 0.8875 (mt) cc_final: 0.8664 (mt) REVERT: C 224 LYS cc_start: 0.8974 (mttp) cc_final: 0.8754 (mttm) REVERT: D 224 LYS cc_start: 0.8974 (mttp) cc_final: 0.8759 (mttm) REVERT: D 329 ILE cc_start: 0.8871 (mt) cc_final: 0.8660 (mt) outliers start: 41 outliers final: 11 residues processed: 156 average time/residue: 0.1348 time to fit residues: 29.4409 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 : 0.486 ------------------------------------------------------------------------------- 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: 3.9990 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.159874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.122895 restraints weight = 15760.270| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.23 r_work: 0.2989 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13596 Z= 0.134 Angle : 0.654 8.700 18304 Z= 0.308 Chirality : 0.043 0.198 2092 Planarity : 0.005 0.052 2196 Dihedral : 23.274 170.361 2516 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.85 % Allowed : 19.59 % Favored : 77.55 % 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 aren not related in a simple way. whole: -0.67 (0.22), residues: 1540 helix: 0.44 (0.18), residues: 1008 sheet: -1.82 (0.45), residues: 116 loop : -2.06 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 111 TYR 0.010 0.001 TYR A 175 PHE 0.006 0.001 PHE B 397 TRP 0.005 0.001 TRP D 155 HIS 0.002 0.000 HIS C 281 Details of bonding type rmsd covalent geometry : bond 0.00313 (13596) covalent geometry : angle 0.65418 (18304) hydrogen bonds : bond 0.03481 ( 680) hydrogen bonds : angle 4.00232 ( 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 162 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.500 Fit side-chains REVERT: A 373 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6261 (mt) REVERT: B 329 ILE cc_start: 0.8907 (mt) cc_final: 0.8702 (mt) REVERT: B 373 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6245 (mt) REVERT: C 373 LEU cc_start: 0.6674 (OUTLIER) cc_final: 0.6265 (mt) REVERT: D 373 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6269 (mt) outliers start: 38 outliers final: 14 residues processed: 154 average time/residue: 0.1236 time to fit residues: 27.3290 Evaluate side-chains 120 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 26 TYR 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 295 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 295 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 295 VAL Chi-restraints excluded: chain D residue 373 LEU 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: 1.9990 chunk 72 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 89 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.158708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.121447 restraints weight = 15833.968| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.30 r_work: 0.2967 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13596 Z= 0.130 Angle : 0.641 9.240 18304 Z= 0.299 Chirality : 0.042 0.182 2092 Planarity : 0.005 0.059 2196 Dihedral : 21.935 175.366 2516 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.85 % Allowed : 20.87 % Favored : 76.28 % 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 aren not related in a simple way. whole: -0.16 (0.23), residues: 1540 helix: 0.74 (0.18), residues: 1008 sheet: -1.57 (0.44), residues: 116 loop : -1.64 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 311 TYR 0.011 0.001 TYR A 175 PHE 0.007 0.001 PHE C 36 TRP 0.005 0.001 TRP A 155 HIS 0.002 0.000 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00303 (13596) covalent geometry : angle 0.64060 (18304) hydrogen bonds : bond 0.03365 ( 680) hydrogen bonds : angle 3.76946 ( 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 153 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.501 Fit side-chains REVERT: A 22 VAL cc_start: 0.8111 (OUTLIER) cc_final: 0.7899 (t) REVERT: A 362 GLU cc_start: 0.8198 (pt0) cc_final: 0.7834 (mt-10) REVERT: B 22 VAL cc_start: 0.8066 (OUTLIER) cc_final: 0.7861 (t) REVERT: B 362 GLU cc_start: 0.8195 (pt0) cc_final: 0.7833 (mt-10) REVERT: C 362 GLU cc_start: 0.8192 (pt0) cc_final: 0.7833 (mt-10) REVERT: C 373 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6134 (mt) REVERT: D 373 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6137 (mt) outliers start: 38 outliers final: 20 residues processed: 149 average time/residue: 0.1168 time to fit residues: 25.6816 Evaluate side-chains 125 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 295 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 22 VAL 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 389 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 26 TYR 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 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: 4.9990 chunk 147 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.151721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.112775 restraints weight = 16050.397| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.71 r_work: 0.2804 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13596 Z= 0.199 Angle : 0.700 8.633 18304 Z= 0.333 Chirality : 0.045 0.187 2092 Planarity : 0.005 0.056 2196 Dihedral : 21.501 175.931 2516 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.20 % Allowed : 19.89 % Favored : 75.90 % 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 aren not related in a simple way. whole: -0.17 (0.22), residues: 1540 helix: 0.66 (0.17), residues: 1004 sheet: -1.40 (0.44), residues: 116 loop : -1.43 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 311 TYR 0.014 0.001 TYR B 175 PHE 0.007 0.001 PHE A 365 TRP 0.007 0.001 TRP B 155 HIS 0.003 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00496 (13596) covalent geometry : angle 0.69958 (18304) hydrogen bonds : bond 0.04104 ( 680) hydrogen bonds : angle 3.87077 ( 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 168 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 112 time to evaluate : 0.558 Fit side-chains REVERT: A 22 VAL cc_start: 0.8272 (t) cc_final: 0.8047 (t) REVERT: A 362 GLU cc_start: 0.8337 (pt0) cc_final: 0.7896 (mt-10) REVERT: A 369 MET cc_start: 0.8466 (mmm) cc_final: 0.8062 (mtm) REVERT: A 373 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6053 (mt) REVERT: B 22 VAL cc_start: 0.8259 (t) cc_final: 0.8033 (t) REVERT: B 362 GLU cc_start: 0.8353 (pt0) cc_final: 0.7916 (mt-10) REVERT: B 369 MET cc_start: 0.8467 (mmm) cc_final: 0.8063 (mtm) REVERT: B 373 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6100 (mt) REVERT: C 362 GLU cc_start: 0.8324 (pt0) cc_final: 0.7926 (mt-10) REVERT: D 362 GLU cc_start: 0.8333 (pt0) cc_final: 0.7896 (mt-10) outliers start: 56 outliers final: 40 residues processed: 163 average time/residue: 0.0958 time to fit residues: 23.9541 Evaluate side-chains 140 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 98 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 124 ARG Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 294 ASP 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 113 LEU Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 294 ASP 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 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 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 113 LEU Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 334 MET Chi-restraints excluded: chain D residue 346 VAL 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: 0.7980 chunk 32 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.157154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.119667 restraints weight = 15966.045| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.38 r_work: 0.2937 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13596 Z= 0.120 Angle : 0.631 9.892 18304 Z= 0.294 Chirality : 0.041 0.165 2092 Planarity : 0.005 0.055 2196 Dihedral : 20.169 177.062 2516 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.30 % Allowed : 21.85 % Favored : 74.85 % 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 aren not related in a simple way. whole: 0.21 (0.23), residues: 1540 helix: 0.89 (0.18), residues: 1008 sheet: -1.34 (0.45), residues: 116 loop : -1.13 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 311 TYR 0.009 0.001 TYR A 259 PHE 0.006 0.001 PHE D 36 TRP 0.003 0.001 TRP C 176 HIS 0.001 0.000 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00274 (13596) covalent geometry : angle 0.63145 (18304) hydrogen bonds : bond 0.03305 ( 680) hydrogen bonds : angle 3.64080 ( 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 159 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 0.415 Fit side-chains REVERT: A 22 VAL cc_start: 0.8189 (OUTLIER) cc_final: 0.7970 (t) REVERT: A 362 GLU cc_start: 0.8210 (pt0) cc_final: 0.7843 (mt-10) REVERT: A 369 MET cc_start: 0.8315 (mmm) cc_final: 0.7862 (mtm) REVERT: A 373 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6067 (mt) REVERT: B 22 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7969 (t) REVERT: B 362 GLU cc_start: 0.8183 (pt0) cc_final: 0.7818 (mt-10) REVERT: B 369 MET cc_start: 0.8311 (mmm) cc_final: 0.7861 (mtm) REVERT: B 373 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6083 (mt) REVERT: C 57 ASP cc_start: 0.6779 (t70) cc_final: 0.6540 (t70) REVERT: C 362 GLU cc_start: 0.8172 (pt0) cc_final: 0.7816 (mt-10) REVERT: C 373 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6059 (mt) REVERT: D 57 ASP cc_start: 0.6829 (t70) cc_final: 0.6598 (t70) REVERT: D 362 GLU cc_start: 0.8197 (pt0) cc_final: 0.7842 (mt-10) REVERT: D 373 LEU cc_start: 0.6535 (OUTLIER) cc_final: 0.6077 (mt) outliers start: 44 outliers final: 15 residues processed: 155 average time/residue: 0.1089 time to fit residues: 24.7284 Evaluate side-chains 124 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 157 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 26 TYR 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 157 SER 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 157 SER 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: 0.9980 chunk 115 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.153630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.114974 restraints weight = 16063.185| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.57 r_work: 0.2842 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3566 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= 0.135 Angle : 0.639 9.354 18304 Z= 0.299 Chirality : 0.042 0.165 2092 Planarity : 0.005 0.057 2196 Dihedral : 19.661 167.922 2516 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.63 % Allowed : 22.22 % Favored : 75.15 % 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 aren not related in a simple way. whole: 0.30 (0.23), residues: 1540 helix: 0.92 (0.18), residues: 1012 sheet: -1.23 (0.46), residues: 116 loop : -1.00 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 111 TYR 0.011 0.001 TYR D 175 PHE 0.007 0.001 PHE D 36 TRP 0.003 0.001 TRP A 155 HIS 0.002 0.000 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00322 (13596) covalent geometry : angle 0.63888 (18304) hydrogen bonds : bond 0.03465 ( 680) hydrogen bonds : angle 3.60378 ( 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 152 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.335 Fit side-chains REVERT: A 22 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.8053 (t) REVERT: A 362 GLU cc_start: 0.8329 (pt0) cc_final: 0.7905 (mt-10) REVERT: A 369 MET cc_start: 0.8365 (mmm) cc_final: 0.7962 (mtm) REVERT: A 373 LEU cc_start: 0.6510 (OUTLIER) cc_final: 0.6050 (mt) REVERT: B 22 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.8030 (t) REVERT: B 362 GLU cc_start: 0.8316 (pt0) cc_final: 0.7884 (mt-10) REVERT: B 369 MET cc_start: 0.8418 (mmm) cc_final: 0.8015 (mtm) REVERT: B 373 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6071 (mt) REVERT: C 362 GLU cc_start: 0.8296 (pt0) cc_final: 0.7874 (mt-10) REVERT: C 373 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6018 (mt) REVERT: D 57 ASP cc_start: 0.6867 (t70) cc_final: 0.6604 (t70) REVERT: D 362 GLU cc_start: 0.8330 (pt0) cc_final: 0.7906 (mt-10) REVERT: D 373 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6073 (mt) outliers start: 35 outliers final: 18 residues processed: 146 average time/residue: 0.1022 time to fit residues: 22.3828 Evaluate side-chains 135 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 157 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 26 TYR 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 157 SER 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 124 ARG Chi-restraints excluded: chain D residue 157 SER 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.6669 > 50: distance: 8 - 18: 11.692 distance: 18 - 19: 10.069 distance: 19 - 20: 23.225 distance: 20 - 21: 12.465 distance: 20 - 22: 19.928 distance: 22 - 23: 5.913 distance: 22 - 28: 11.321 distance: 23 - 24: 7.321 distance: 23 - 26: 15.343 distance: 24 - 25: 18.398 distance: 24 - 29: 13.457 distance: 26 - 27: 16.631 distance: 27 - 28: 23.193 distance: 29 - 30: 5.303 distance: 30 - 31: 4.034 distance: 31 - 32: 9.596 distance: 31 - 33: 14.041 distance: 33 - 34: 14.397 distance: 34 - 35: 3.200 distance: 34 - 37: 4.962 distance: 35 - 36: 25.233 distance: 35 - 42: 6.820 distance: 37 - 38: 6.913 distance: 38 - 39: 4.310 distance: 39 - 41: 6.583 distance: 42 - 43: 8.031 distance: 43 - 44: 7.896 distance: 43 - 46: 11.029 distance: 44 - 45: 11.001 distance: 44 - 54: 8.347 distance: 46 - 47: 8.294 distance: 47 - 48: 4.421 distance: 47 - 49: 6.363 distance: 48 - 50: 10.225 distance: 49 - 51: 7.061 distance: 50 - 52: 12.160 distance: 51 - 52: 11.478 distance: 54 - 55: 4.425 distance: 55 - 56: 4.710 distance: 56 - 57: 19.428 distance: 56 - 62: 12.692 distance: 58 - 59: 7.754 distance: 58 - 60: 6.471 distance: 59 - 61: 10.009 distance: 62 - 63: 8.547 distance: 63 - 64: 5.514 distance: 64 - 65: 6.151 distance: 64 - 70: 12.159 distance: 65 - 146: 10.640 distance: 66 - 67: 4.129 distance: 66 - 68: 5.967 distance: 67 - 69: 10.237 distance: 70 - 71: 13.300 distance: 71 - 72: 13.988 distance: 71 - 74: 7.590 distance: 72 - 73: 19.581 distance: 72 - 81: 37.740 distance: 74 - 75: 6.416 distance: 75 - 76: 6.029 distance: 76 - 77: 4.786 distance: 81 - 82: 14.097 distance: 82 - 83: 24.724 distance: 82 - 85: 20.090 distance: 83 - 84: 39.654 distance: 83 - 86: 14.320 distance: 86 - 87: 27.184 distance: 87 - 88: 23.490 distance: 88 - 89: 12.095 distance: 88 - 90: 15.973