Starting phenix.real_space_refine on Fri Jul 3 10:21:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vxz_21453/07_2026/6vxz_21453.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxz_21453/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vxz_21453/07_2026/6vxz_21453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxz_21453/07_2026/6vxz_21453.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vxz_21453/07_2026/6vxz_21453.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vxz_21453/07_2026/6vxz_21453.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vxz_21453/07_2026/6vxz_21453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxz_21453/07_2026/6vxz_21453.cif" } 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-dev-6108/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: {'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: 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: 2.20, per 1000 atoms: 0.17 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: 0.88 Conformation dependent library (CDL) restraints added in 512.4 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: 0.34 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: 2.01 Time building geometry restraints manager: 1.18 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 - 30.79: 7704 30.79 - 61.58: 520 61.58 - 92.37: 40 92.37 - 123.16: 8 123.16 - 153.95: 8 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: 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: 1.260 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 10.480 Find NCS groups from input model: 0.090 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.180 ------------------------------------------------------------------------------- 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= 0.503 Angle : 1.068 10.523 18304 Z= 0.563 Chirality : 0.057 0.314 2092 Planarity : 0.008 0.150 2196 Dihedral : 19.896 153.952 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 0.01107 / 0.50 (13596) covalent geometry : angle 1.06770 / 0.56 (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 : 0.469 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: 0.1122 time to fit residues: 29.0069 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 : 0.330 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.163113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129774 restraints weight = 15332.549| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.11 r_work: 0.3049 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1836 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= 0.144 Angle : 0.684 9.090 18304 Z= 0.323 Chirality : 0.044 0.186 2092 Planarity : 0.005 0.047 2196 Dihedral : 18.990 138.752 2442 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.08 % Allowed : 18.92 % Favored : 78.00 % 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: -1.55 (0.22), residues: 1540 helix: -0.18 (0.17), residues: 1008 sheet: -1.92 (0.47), residues: 112 loop : -2.66 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 382 TYR 0.013 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 D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (13596) covalent geometry : angle 0.68434 / 0.32 (18304) hydrogen bonds : bond 0.03703 / 2.44 ( 680) hydrogen bonds : angle 4.53021 / 3.25 ( 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 161 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.342 Fit side-chains REVERT: A 224 LYS cc_start: 0.8977 (mttp) cc_final: 0.8745 (mttm) REVERT: A 329 ILE cc_start: 0.8891 (mt) cc_final: 0.8682 (mt) REVERT: B 224 LYS cc_start: 0.8969 (mttp) cc_final: 0.8748 (mttm) REVERT: B 329 ILE cc_start: 0.8886 (mt) cc_final: 0.8676 (mt) REVERT: C 224 LYS cc_start: 0.8974 (mttp) cc_final: 0.8764 (mttm) REVERT: D 224 LYS cc_start: 0.8976 (mttp) cc_final: 0.8761 (mttm) REVERT: D 329 ILE cc_start: 0.8880 (mt) cc_final: 0.8673 (mt) outliers start: 41 outliers final: 11 residues processed: 157 average time/residue: 0.1125 time to fit residues: 24.8799 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 : 0.431 ------------------------------------------------------------------------------- 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: 0.0050 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 69 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.162379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125537 restraints weight = 15644.219| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.36 r_work: 0.3019 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2436 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= 0.116 Angle : 0.637 9.315 18304 Z= 0.297 Chirality : 0.042 0.194 2092 Planarity : 0.004 0.050 2196 Dihedral : 16.665 133.700 2396 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.18 % Allowed : 19.82 % Favored : 78.00 % 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: -0.60 (0.22), residues: 1540 helix: 0.52 (0.18), residues: 1004 sheet: -1.78 (0.44), residues: 116 loop : -2.08 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 111 TYR 0.009 0.001 TYR B 175 PHE 0.005 0.001 PHE D 40 TRP 0.002 0.001 TRP B 155 HIS 0.001 0.000 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (13596) covalent geometry : angle 0.63689 / 0.30 (18304) hydrogen bonds : bond 0.03227 / 2.12 ( 680) hydrogen bonds : angle 3.95110 / 2.83 ( 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 167 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.373 Fit side-chains REVERT: A 373 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6227 (mt) REVERT: B 373 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6233 (mt) REVERT: C 373 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6232 (mt) REVERT: D 373 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6228 (mt) outliers start: 29 outliers final: 5 residues processed: 155 average time/residue: 0.1047 time to fit residues: 23.6800 Evaluate side-chains 112 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 26 TYR 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 373 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.0010 chunk 145 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.158143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.121390 restraints weight = 15827.913| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.25 r_work: 0.2959 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13596 Z= 0.136 Angle : 0.640 9.052 18304 Z= 0.300 Chirality : 0.042 0.185 2092 Planarity : 0.005 0.062 2196 Dihedral : 15.726 134.345 2396 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.55 % Allowed : 21.17 % 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 are not related in a simple way. whole: -0.12 (0.23), residues: 1540 helix: 0.75 (0.18), residues: 1012 sheet: -1.54 (0.44), residues: 116 loop : -1.57 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 311 TYR 0.012 0.001 TYR A 175 PHE 0.007 0.001 PHE D 366 TRP 0.006 0.001 TRP B 155 HIS 0.002 0.000 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (13596) covalent geometry : angle 0.63967 / 0.30 (18304) hydrogen bonds : bond 0.03447 / 2.25 ( 680) hydrogen bonds : angle 3.76225 / 2.70 ( 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 158 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.488 Fit side-chains REVERT: A 22 VAL cc_start: 0.8102 (OUTLIER) cc_final: 0.7897 (t) REVERT: A 230 LEU cc_start: 0.8752 (mm) cc_final: 0.8534 (mt) REVERT: B 230 LEU cc_start: 0.8752 (mm) cc_final: 0.8534 (mt) REVERT: B 362 GLU cc_start: 0.8213 (pt0) cc_final: 0.7851 (mt-10) REVERT: C 230 LEU cc_start: 0.8754 (mm) cc_final: 0.8539 (mt) REVERT: C 362 GLU cc_start: 0.8129 (pt0) cc_final: 0.7839 (mt-10) REVERT: D 230 LEU cc_start: 0.8754 (mm) cc_final: 0.8536 (mt) outliers start: 34 outliers final: 22 residues processed: 152 average time/residue: 0.0988 time to fit residues: 22.4358 Evaluate side-chains 134 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 372 ILE 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 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 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 372 ILE Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.158 > 50: distance: 36 - 60: 8.161 distance: 40 - 45: 5.547 distance: 41 - 68: 5.659 distance: 45 - 46: 3.154 distance: 45 - 51: 5.869 distance: 46 - 47: 5.385 distance: 46 - 49: 4.603 distance: 47 - 48: 15.522 distance: 47 - 52: 10.155 distance: 48 - 76: 12.581 distance: 49 - 50: 11.773 distance: 50 - 51: 9.043 distance: 52 - 53: 4.730 distance: 53 - 54: 7.344 distance: 53 - 56: 8.947 distance: 54 - 55: 3.902 distance: 54 - 60: 11.097 distance: 55 - 81: 12.229 distance: 56 - 57: 8.732 distance: 57 - 58: 7.247 distance: 60 - 61: 7.970 distance: 61 - 62: 3.196 distance: 61 - 64: 7.859 distance: 62 - 63: 13.813 distance: 62 - 68: 8.136 distance: 64 - 65: 16.814 distance: 65 - 66: 6.897 distance: 65 - 67: 11.632 distance: 69 - 70: 5.253 distance: 69 - 72: 4.026 distance: 70 - 71: 13.997 distance: 70 - 76: 7.869 distance: 72 - 73: 9.812 distance: 73 - 74: 8.716 distance: 73 - 75: 10.235 distance: 76 - 77: 5.925 distance: 77 - 80: 6.684 distance: 78 - 79: 5.256 distance: 78 - 81: 6.892 distance: 81 - 82: 11.781 distance: 82 - 83: 11.387 distance: 82 - 85: 6.232 distance: 83 - 84: 10.597 distance: 83 - 86: 3.112 distance: 86 - 87: 16.231 distance: 87 - 88: 23.181 distance: 87 - 90: 20.006 distance: 88 - 89: 5.856 distance: 88 - 94: 19.664 distance: 90 - 91: 23.291 distance: 91 - 92: 18.560 distance: 91 - 93: 23.128 distance: 94 - 100: 9.903 distance: 95 - 96: 11.653 distance: 95 - 98: 14.635 distance: 96 - 97: 40.762 distance: 96 - 101: 11.362 distance: 98 - 99: 20.949 distance: 99 - 100: 14.642 distance: 101 - 102: 23.497 distance: 102 - 103: 7.364 distance: 102 - 105: 18.743 distance: 103 - 104: 19.098 distance: 103 - 109: 15.222 distance: 105 - 106: 21.841 distance: 106 - 107: 33.353 distance: 106 - 108: 10.411 distance: 109 - 110: 7.823 distance: 110 - 111: 7.328 distance: 110 - 113: 7.611 distance: 111 - 112: 18.672 distance: 111 - 117: 6.835 distance: 112 - 139: 16.081 distance: 113 - 114: 12.361 distance: 114 - 115: 21.314 distance: 114 - 116: 25.742