Starting phenix.real_space_refine on Thu Jul 31 16:34:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vxz_21453/07_2025/6vxz_21453.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vxz_21453/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6vxz_21453/07_2025/6vxz_21453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vxz_21453/07_2025/6vxz_21453.map" model { file = "/net/cci-nas-00/data/ceres_data/6vxz_21453/07_2025/6vxz_21453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vxz_21453/07_2025/6vxz_21453.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, D Time building chain proxies: 7.21, per 1000 atoms: 0.54 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: 3.46 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.36 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: 3.60 Time building geometry restraints manager: 3.82 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.400 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: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 30.360 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.570 ------------------------------------------------------------------------------- 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 : 12.61 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.002 TRP B 18 HIS 0.003 0.001 HIS B 232 PHE 0.011 0.001 PHE A 397 TYR 0.014 0.001 TYR D 175 ARG 0.003 0.001 ARG D 399 Details of bonding type rmsd hydrogen bonds : bond 0.14080 ( 680) hydrogen bonds : angle 7.02920 ( 1956) covalent geometry : bond 0.01107 (13596) covalent geometry : angle 1.06770 (18304) *********************** 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 : 1.316 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: 0.2790 time to fit residues: 71.0505 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 : 1.507 ------------------------------------------------------------------------------- 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 128 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3808 r_free = 0.3808 target = 0.161781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.126908 restraints weight = 15235.169| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.24 r_work: 0.3022 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13596 Z= 0.146 Angle : 0.697 9.178 18304 Z= 0.328 Chirality : 0.044 0.191 2092 Planarity : 0.005 0.047 2196 Dihedral : 25.418 165.737 2562 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.15 % Allowed : 18.69 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1540 helix: -0.15 (0.17), residues: 1008 sheet: -1.88 (0.47), residues: 112 loop : -2.64 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 155 HIS 0.002 0.001 HIS C 281 PHE 0.005 0.001 PHE B 40 TYR 0.013 0.001 TYR A 25 ARG 0.003 0.000 ARG D 382 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 680) hydrogen bonds : angle 4.50900 ( 1956) covalent geometry : bond 0.00342 (13596) covalent geometry : angle 0.69733 (18304) *********************** 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: 42 poor density : 119 time to evaluate : 1.469 Fit side-chains REVERT: A 224 LYS cc_start: 0.8968 (mttp) cc_final: 0.8744 (mttm) REVERT: A 329 ILE cc_start: 0.8855 (mt) cc_final: 0.8644 (mt) REVERT: B 224 LYS cc_start: 0.8960 (mttp) cc_final: 0.8736 (mttm) REVERT: B 329 ILE cc_start: 0.8852 (mt) cc_final: 0.8641 (mt) REVERT: C 224 LYS cc_start: 0.8959 (mttp) cc_final: 0.8757 (mttm) REVERT: D 224 LYS cc_start: 0.8967 (mttp) cc_final: 0.8751 (mttm) REVERT: D 329 ILE cc_start: 0.8847 (mt) cc_final: 0.8635 (mt) outliers start: 42 outliers final: 11 residues processed: 156 average time/residue: 0.3199 time to fit residues: 69.7329 Evaluate side-chains 119 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 42 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.149550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.112579 restraints weight = 16314.538| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.60 r_work: 0.2815 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 13596 Z= 0.325 Angle : 0.829 8.368 18304 Z= 0.400 Chirality : 0.051 0.246 2092 Planarity : 0.006 0.055 2196 Dihedral : 25.129 169.010 2516 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.80 % Allowed : 18.39 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.22), residues: 1540 helix: -0.04 (0.17), residues: 1012 sheet: -1.50 (0.50), residues: 116 loop : -2.46 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 155 HIS 0.003 0.001 HIS B 281 PHE 0.010 0.002 PHE D 365 TYR 0.016 0.002 TYR B 175 ARG 0.005 0.001 ARG C 111 Details of bonding type rmsd hydrogen bonds : bond 0.05138 ( 680) hydrogen bonds : angle 4.44085 ( 1956) covalent geometry : bond 0.00813 (13596) covalent geometry : angle 0.82898 (18304) *********************** 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 173 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 109 time to evaluate : 1.408 Fit side-chains REVERT: A 22 VAL cc_start: 0.8295 (t) cc_final: 0.8057 (t) REVERT: A 346 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8494 (t) REVERT: A 398 ASP cc_start: 0.8337 (t0) cc_final: 0.8103 (p0) REVERT: B 22 VAL cc_start: 0.8346 (t) cc_final: 0.8113 (t) REVERT: B 346 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8492 (t) REVERT: B 398 ASP cc_start: 0.8334 (t0) cc_final: 0.8111 (p0) REVERT: C 22 VAL cc_start: 0.8346 (t) cc_final: 0.8120 (t) REVERT: C 25 TYR cc_start: 0.8300 (t80) cc_final: 0.8072 (t80) REVERT: C 346 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8481 (t) REVERT: C 362 GLU cc_start: 0.8231 (pt0) cc_final: 0.7843 (mt-10) REVERT: C 398 ASP cc_start: 0.8329 (t0) cc_final: 0.8110 (p0) REVERT: D 22 VAL cc_start: 0.8350 (t) cc_final: 0.8114 (t) REVERT: D 346 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8499 (t) REVERT: D 362 GLU cc_start: 0.8246 (pt0) cc_final: 0.7857 (mt-10) REVERT: D 369 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7992 (mtm) REVERT: D 398 ASP cc_start: 0.8341 (t0) cc_final: 0.8112 (p0) outliers start: 64 outliers final: 33 residues processed: 160 average time/residue: 0.2362 time to fit residues: 56.8999 Evaluate side-chains 143 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL 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 222 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 PHE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 124 ARG Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 365 PHE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 14 VAL 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 222 VAL 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 365 PHE Chi-restraints excluded: chain D residue 369 MET Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 150 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 43 optimal weight: 0.0040 chunk 103 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 overall best weight: 0.4970 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.156698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118037 restraints weight = 15776.127| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.52 r_work: 0.2929 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13596 Z= 0.113 Angle : 0.643 10.033 18304 Z= 0.300 Chirality : 0.041 0.185 2092 Planarity : 0.005 0.062 2196 Dihedral : 22.549 174.741 2516 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.23 % Allowed : 20.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.23), residues: 1540 helix: 0.59 (0.18), residues: 1004 sheet: -1.40 (0.48), residues: 116 loop : -1.73 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 176 HIS 0.001 0.000 HIS D 281 PHE 0.004 0.001 PHE B 36 TYR 0.010 0.001 TYR A 259 ARG 0.003 0.000 ARG C 111 Details of bonding type rmsd hydrogen bonds : bond 0.03264 ( 680) hydrogen bonds : angle 3.88023 ( 1956) covalent geometry : bond 0.00243 (13596) covalent geometry : angle 0.64331 (18304) *********************** 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 182 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 1.340 Fit side-chains REVERT: A 22 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7891 (t) REVERT: A 230 LEU cc_start: 0.8808 (mm) cc_final: 0.8571 (mt) REVERT: A 307 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.6253 (mm-30) REVERT: A 362 GLU cc_start: 0.8218 (pt0) cc_final: 0.7695 (mt-10) REVERT: A 373 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6071 (mt) REVERT: B 22 VAL cc_start: 0.8119 (OUTLIER) cc_final: 0.7898 (t) REVERT: B 230 LEU cc_start: 0.8824 (mm) cc_final: 0.8499 (mt) REVERT: B 307 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.6244 (mm-30) REVERT: B 362 GLU cc_start: 0.8220 (pt0) cc_final: 0.7694 (mt-10) REVERT: B 373 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6072 (mt) REVERT: C 22 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7891 (t) REVERT: C 230 LEU cc_start: 0.8827 (mm) cc_final: 0.8501 (mt) REVERT: C 362 GLU cc_start: 0.8216 (pt0) cc_final: 0.7692 (mt-10) REVERT: C 373 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6072 (mt) REVERT: D 22 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7889 (t) REVERT: D 230 LEU cc_start: 0.8806 (mm) cc_final: 0.8567 (mt) REVERT: D 307 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.6249 (mm-30) REVERT: D 362 GLU cc_start: 0.8203 (pt0) cc_final: 0.7687 (mt-10) REVERT: D 373 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6041 (mt) outliers start: 43 outliers final: 9 residues processed: 178 average time/residue: 0.2538 time to fit residues: 66.3345 Evaluate side-chains 140 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 307 GLU 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 307 GLU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 22 VAL 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 22 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 307 GLU 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 35 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 0.0970 chunk 115 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.152654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.114706 restraints weight = 16192.264| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.31 r_work: 0.2882 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13596 Z= 0.159 Angle : 0.671 8.789 18304 Z= 0.317 Chirality : 0.043 0.174 2092 Planarity : 0.005 0.057 2196 Dihedral : 21.426 178.366 2516 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.90 % Allowed : 21.02 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1540 helix: 0.66 (0.18), residues: 1004 sheet: -1.29 (0.47), residues: 116 loop : -1.41 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 155 HIS 0.003 0.001 HIS C 281 PHE 0.006 0.001 PHE A 36 TYR 0.014 0.001 TYR A 175 ARG 0.002 0.000 ARG C 377 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 680) hydrogen bonds : angle 3.80183 ( 1956) covalent geometry : bond 0.00386 (13596) covalent geometry : angle 0.67149 (18304) *********************** 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 165 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 113 time to evaluate : 1.499 Fit side-chains REVERT: A 22 VAL cc_start: 0.8194 (t) cc_final: 0.7968 (t) REVERT: A 230 LEU cc_start: 0.8937 (mm) cc_final: 0.8609 (mt) REVERT: A 362 GLU cc_start: 0.8230 (pt0) cc_final: 0.7811 (mt-10) REVERT: A 380 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8172 (t) REVERT: B 22 VAL cc_start: 0.8204 (t) cc_final: 0.7977 (t) REVERT: B 230 LEU cc_start: 0.8938 (mm) cc_final: 0.8615 (mt) REVERT: B 362 GLU cc_start: 0.8223 (pt0) cc_final: 0.7802 (mt-10) REVERT: B 380 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8155 (t) REVERT: C 22 VAL cc_start: 0.8199 (t) cc_final: 0.7973 (t) REVERT: C 230 LEU cc_start: 0.8953 (mm) cc_final: 0.8634 (mt) REVERT: C 346 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8444 (t) REVERT: C 362 GLU cc_start: 0.8199 (pt0) cc_final: 0.7776 (mt-10) REVERT: C 380 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8160 (t) REVERT: D 22 VAL cc_start: 0.8186 (t) cc_final: 0.7960 (t) REVERT: D 230 LEU cc_start: 0.8941 (mm) cc_final: 0.8612 (mt) REVERT: D 346 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8457 (t) REVERT: D 362 GLU cc_start: 0.8203 (pt0) cc_final: 0.7776 (mt-10) REVERT: D 373 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6125 (mt) REVERT: D 380 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8154 (t) outliers start: 52 outliers final: 24 residues processed: 161 average time/residue: 0.2235 time to fit residues: 55.6575 Evaluate side-chains 141 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 380 THR 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 38 optimal weight: 10.0000 chunk 54 optimal weight: 0.1980 chunk 100 optimal weight: 0.0980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.154902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.116857 restraints weight = 16326.323| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.37 r_work: 0.2912 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13596 Z= 0.130 Angle : 0.643 9.602 18304 Z= 0.300 Chirality : 0.041 0.164 2092 Planarity : 0.005 0.056 2196 Dihedral : 19.777 174.175 2516 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.63 % Allowed : 22.67 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.23), residues: 1540 helix: 0.82 (0.18), residues: 1004 sheet: -1.26 (0.46), residues: 116 loop : -1.20 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 155 HIS 0.002 0.000 HIS A 281 PHE 0.006 0.001 PHE A 36 TYR 0.010 0.001 TYR D 175 ARG 0.002 0.000 ARG C 111 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 680) hydrogen bonds : angle 3.68355 ( 1956) covalent geometry : bond 0.00308 (13596) covalent geometry : angle 0.64294 (18304) *********************** 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 162 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 1.359 Fit side-chains REVERT: A 22 VAL cc_start: 0.8185 (t) cc_final: 0.7967 (t) REVERT: A 230 LEU cc_start: 0.8906 (mm) cc_final: 0.8596 (mt) REVERT: A 362 GLU cc_start: 0.8241 (pt0) cc_final: 0.7829 (mt-10) REVERT: A 373 LEU cc_start: 0.6520 (OUTLIER) cc_final: 0.6047 (mt) REVERT: B 22 VAL cc_start: 0.8193 (t) cc_final: 0.7972 (t) REVERT: B 230 LEU cc_start: 0.8910 (mm) cc_final: 0.8602 (mt) REVERT: B 362 GLU cc_start: 0.8234 (pt0) cc_final: 0.7815 (mt-10) REVERT: B 373 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6066 (mt) REVERT: C 22 VAL cc_start: 0.8207 (t) cc_final: 0.7996 (t) REVERT: C 230 LEU cc_start: 0.8907 (mm) cc_final: 0.8598 (mt) REVERT: C 362 GLU cc_start: 0.8217 (pt0) cc_final: 0.7790 (mt-10) REVERT: C 373 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6066 (mt) REVERT: D 22 VAL cc_start: 0.8180 (t) cc_final: 0.7961 (t) REVERT: D 230 LEU cc_start: 0.8908 (mm) cc_final: 0.8597 (mt) REVERT: D 362 GLU cc_start: 0.8220 (pt0) cc_final: 0.7800 (mt-10) REVERT: D 373 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6090 (mt) REVERT: D 380 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8176 (t) outliers start: 35 outliers final: 16 residues processed: 158 average time/residue: 0.2475 time to fit residues: 57.9916 Evaluate side-chains 134 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 380 THR 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 132 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 134 optimal weight: 0.1980 chunk 70 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.155076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.116543 restraints weight = 16172.992| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.25 r_work: 0.2921 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13596 Z= 0.122 Angle : 0.632 9.484 18304 Z= 0.294 Chirality : 0.041 0.171 2092 Planarity : 0.005 0.057 2196 Dihedral : 18.727 160.919 2516 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.25 % Allowed : 23.35 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1540 helix: 0.96 (0.18), residues: 1004 sheet: -1.26 (0.46), residues: 116 loop : -1.05 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 176 HIS 0.002 0.000 HIS A 281 PHE 0.007 0.001 PHE B 36 TYR 0.011 0.001 TYR D 175 ARG 0.004 0.000 ARG B 111 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 680) hydrogen bonds : angle 3.58904 ( 1956) covalent geometry : bond 0.00283 (13596) covalent geometry : angle 0.63186 (18304) *********************** 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 149 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 1.380 Fit side-chains REVERT: A 230 LEU cc_start: 0.8856 (mm) cc_final: 0.8637 (mt) REVERT: A 362 GLU cc_start: 0.8231 (pt0) cc_final: 0.7797 (mt-10) REVERT: A 373 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6065 (mt) REVERT: B 22 VAL cc_start: 0.8166 (t) cc_final: 0.7954 (t) REVERT: B 230 LEU cc_start: 0.8861 (mm) cc_final: 0.8642 (mt) REVERT: B 362 GLU cc_start: 0.8218 (pt0) cc_final: 0.7787 (mt-10) REVERT: B 373 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6067 (mt) REVERT: C 22 VAL cc_start: 0.8158 (t) cc_final: 0.7946 (t) REVERT: C 230 LEU cc_start: 0.8863 (mm) cc_final: 0.8645 (mt) REVERT: C 362 GLU cc_start: 0.8199 (pt0) cc_final: 0.7771 (mt-10) REVERT: C 373 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6047 (mt) REVERT: C 380 THR cc_start: 0.8235 (t) cc_final: 0.7854 (p) REVERT: D 230 LEU cc_start: 0.8858 (mm) cc_final: 0.8639 (mt) REVERT: D 362 GLU cc_start: 0.8232 (pt0) cc_final: 0.7807 (mt-10) REVERT: D 369 MET cc_start: 0.8255 (mmm) cc_final: 0.7728 (mtm) REVERT: D 373 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6067 (mt) outliers start: 30 outliers final: 20 residues processed: 145 average time/residue: 0.2239 time to fit residues: 49.2191 Evaluate side-chains 140 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 307 GLU 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 58 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 45 optimal weight: 6.9990 chunk 127 optimal weight: 0.0170 chunk 38 optimal weight: 10.0000 chunk 133 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 overall best weight: 0.9020 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.154709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.118482 restraints weight = 16076.457| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.20 r_work: 0.2908 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13596 Z= 0.126 Angle : 0.628 9.197 18304 Z= 0.293 Chirality : 0.041 0.163 2092 Planarity : 0.005 0.059 2196 Dihedral : 18.143 147.588 2516 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.33 % Allowed : 23.27 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1540 helix: 1.11 (0.18), residues: 988 sheet: -1.29 (0.46), residues: 116 loop : -0.81 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 155 HIS 0.002 0.000 HIS C 281 PHE 0.007 0.001 PHE A 36 TYR 0.011 0.001 TYR D 175 ARG 0.006 0.000 ARG B 311 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 680) hydrogen bonds : angle 3.54780 ( 1956) covalent geometry : bond 0.00294 (13596) covalent geometry : angle 0.62793 (18304) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 1.357 Fit side-chains REVERT: A 57 ASP cc_start: 0.6840 (t70) cc_final: 0.6553 (t70) REVERT: A 230 LEU cc_start: 0.8773 (mm) cc_final: 0.8541 (mt) REVERT: A 362 GLU cc_start: 0.8208 (pt0) cc_final: 0.7682 (mt-10) REVERT: A 373 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6007 (mt) REVERT: B 22 VAL cc_start: 0.8019 (t) cc_final: 0.7817 (t) REVERT: B 57 ASP cc_start: 0.6842 (t70) cc_final: 0.6563 (t70) REVERT: B 230 LEU cc_start: 0.8773 (mm) cc_final: 0.8545 (mt) REVERT: B 307 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.6143 (mm-30) REVERT: B 362 GLU cc_start: 0.8198 (pt0) cc_final: 0.7672 (mt-10) REVERT: B 373 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6002 (mt) REVERT: C 22 VAL cc_start: 0.8023 (t) cc_final: 0.7814 (t) REVERT: C 230 LEU cc_start: 0.8776 (mm) cc_final: 0.8550 (mt) REVERT: C 362 GLU cc_start: 0.8183 (pt0) cc_final: 0.7729 (tt0) REVERT: C 373 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.5980 (mt) REVERT: C 380 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.7764 (p) REVERT: D 22 VAL cc_start: 0.8009 (t) cc_final: 0.7808 (t) REVERT: D 57 ASP cc_start: 0.6840 (t70) cc_final: 0.6556 (t70) REVERT: D 230 LEU cc_start: 0.8772 (mm) cc_final: 0.8540 (mt) REVERT: D 362 GLU cc_start: 0.8195 (pt0) cc_final: 0.7680 (mt-10) REVERT: D 369 MET cc_start: 0.8133 (mmm) cc_final: 0.7664 (mtm) REVERT: D 373 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6004 (mt) outliers start: 31 outliers final: 18 residues processed: 159 average time/residue: 0.2345 time to fit residues: 56.4131 Evaluate side-chains 146 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 307 GLU 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 58 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 22 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 65 optimal weight: 0.0060 chunk 98 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 69 optimal weight: 0.0060 chunk 131 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 overall best weight: 0.9216 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.154517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.118553 restraints weight = 15874.772| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.32 r_work: 0.2890 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13596 Z= 0.128 Angle : 0.638 9.059 18304 Z= 0.298 Chirality : 0.042 0.161 2092 Planarity : 0.005 0.061 2196 Dihedral : 17.944 144.711 2516 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.25 % Allowed : 23.87 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.23), residues: 1540 helix: 1.16 (0.18), residues: 992 sheet: -1.30 (0.46), residues: 116 loop : -0.69 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 155 HIS 0.002 0.000 HIS C 281 PHE 0.007 0.001 PHE B 36 TYR 0.011 0.001 TYR D 175 ARG 0.007 0.000 ARG D 311 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 680) hydrogen bonds : angle 3.55142 ( 1956) covalent geometry : bond 0.00304 (13596) covalent geometry : angle 0.63837 (18304) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.407 Fit side-chains REVERT: A 57 ASP cc_start: 0.6862 (t70) cc_final: 0.6586 (t70) REVERT: A 230 LEU cc_start: 0.8816 (mm) cc_final: 0.8594 (mt) REVERT: A 307 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.6155 (mm-30) REVERT: A 362 GLU cc_start: 0.8224 (pt0) cc_final: 0.7774 (tt0) REVERT: A 373 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6016 (mt) REVERT: B 22 VAL cc_start: 0.8073 (t) cc_final: 0.7867 (t) REVERT: B 57 ASP cc_start: 0.6866 (t70) cc_final: 0.6594 (t70) REVERT: B 230 LEU cc_start: 0.8810 (mm) cc_final: 0.8592 (mt) REVERT: B 362 GLU cc_start: 0.8217 (pt0) cc_final: 0.7762 (tt0) REVERT: B 373 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6002 (mt) REVERT: C 22 VAL cc_start: 0.8080 (t) cc_final: 0.7875 (t) REVERT: C 230 LEU cc_start: 0.8818 (mm) cc_final: 0.8598 (mt) REVERT: C 362 GLU cc_start: 0.8188 (pt0) cc_final: 0.7720 (tt0) REVERT: C 373 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.5980 (mt) REVERT: C 380 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.7843 (p) REVERT: D 22 VAL cc_start: 0.8067 (t) cc_final: 0.7858 (t) REVERT: D 230 LEU cc_start: 0.8820 (mm) cc_final: 0.8595 (mt) REVERT: D 307 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.6187 (mm-30) REVERT: D 362 GLU cc_start: 0.8241 (pt0) cc_final: 0.7772 (tt0) REVERT: D 369 MET cc_start: 0.8213 (mmm) cc_final: 0.7761 (mtm) REVERT: D 373 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6010 (mt) outliers start: 30 outliers final: 18 residues processed: 154 average time/residue: 0.2294 time to fit residues: 53.3345 Evaluate side-chains 146 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 124 ARG Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 307 GLU 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 58 ILE Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 307 GLU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 103 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 13 optimal weight: 0.0570 chunk 62 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.155597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.117240 restraints weight = 15988.840| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.41 r_work: 0.2875 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13596 Z= 0.116 Angle : 0.643 12.018 18304 Z= 0.299 Chirality : 0.041 0.157 2092 Planarity : 0.005 0.063 2196 Dihedral : 17.523 141.523 2516 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.65 % Allowed : 24.77 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.23), residues: 1540 helix: 1.34 (0.18), residues: 992 sheet: -1.29 (0.51), residues: 96 loop : -0.53 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 176 HIS 0.001 0.000 HIS A 281 PHE 0.007 0.001 PHE B 36 TYR 0.010 0.001 TYR C 175 ARG 0.007 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03157 ( 680) hydrogen bonds : angle 3.50196 ( 1956) covalent geometry : bond 0.00267 (13596) covalent geometry : angle 0.64321 (18304) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.364 Fit side-chains REVERT: A 57 ASP cc_start: 0.6920 (t70) cc_final: 0.6680 (t70) REVERT: A 230 LEU cc_start: 0.8878 (mm) cc_final: 0.8667 (mt) REVERT: A 362 GLU cc_start: 0.8286 (pt0) cc_final: 0.7866 (tt0) REVERT: A 373 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.5957 (mt) REVERT: B 22 VAL cc_start: 0.8186 (t) cc_final: 0.7981 (t) REVERT: B 57 ASP cc_start: 0.6847 (t70) cc_final: 0.6594 (t70) REVERT: B 230 LEU cc_start: 0.8881 (mm) cc_final: 0.8667 (mt) REVERT: B 307 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.6198 (mm-30) REVERT: B 362 GLU cc_start: 0.8280 (pt0) cc_final: 0.7858 (tt0) REVERT: B 373 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6054 (mt) REVERT: C 22 VAL cc_start: 0.8188 (t) cc_final: 0.7983 (t) REVERT: C 57 ASP cc_start: 0.6845 (t70) cc_final: 0.6584 (t70) REVERT: C 230 LEU cc_start: 0.8883 (mm) cc_final: 0.8670 (mt) REVERT: C 362 GLU cc_start: 0.8331 (pt0) cc_final: 0.7841 (tt0) REVERT: C 373 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.5986 (mt) REVERT: C 380 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7904 (p) REVERT: D 22 VAL cc_start: 0.8184 (t) cc_final: 0.7981 (t) REVERT: D 57 ASP cc_start: 0.6847 (t70) cc_final: 0.6586 (t70) REVERT: D 230 LEU cc_start: 0.8879 (mm) cc_final: 0.8667 (mt) REVERT: D 362 GLU cc_start: 0.8299 (pt0) cc_final: 0.7864 (tt0) REVERT: D 369 MET cc_start: 0.8240 (mmm) cc_final: 0.7797 (mtm) REVERT: D 373 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.6014 (mt) outliers start: 22 outliers final: 14 residues processed: 152 average time/residue: 0.2157 time to fit residues: 50.8584 Evaluate side-chains 144 residues out of total 1332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 157 SER Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 307 GLU 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 157 SER Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 380 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 26 optimal weight: 1.9990 chunk 120 optimal weight: 0.0270 chunk 17 optimal weight: 0.0470 chunk 54 optimal weight: 0.0070 chunk 50 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.157882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.121870 restraints weight = 15918.469| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.21 r_work: 0.2974 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13596 Z= 0.106 Angle : 0.627 11.340 18304 Z= 0.290 Chirality : 0.040 0.149 2092 Planarity : 0.005 0.063 2196 Dihedral : 16.919 138.151 2516 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.80 % Allowed : 24.77 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.23), residues: 1540 helix: 1.52 (0.18), residues: 992 sheet: -1.33 (0.51), residues: 96 loop : -0.35 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 264 HIS 0.001 0.000 HIS D 281 PHE 0.008 0.001 PHE B 36 TYR 0.009 0.001 TYR C 175 ARG 0.007 0.000 ARG D 311 Details of bonding type rmsd hydrogen bonds : bond 0.02881 ( 680) hydrogen bonds : angle 3.44552 ( 1956) covalent geometry : bond 0.00230 (13596) covalent geometry : angle 0.62702 (18304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5773.53 seconds wall clock time: 99 minutes 50.93 seconds (5990.93 seconds total)