Starting phenix.real_space_refine on Sat Aug 23 23:12:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvx_17979/08_2025/8pvx_17979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvx_17979/08_2025/8pvx_17979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pvx_17979/08_2025/8pvx_17979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvx_17979/08_2025/8pvx_17979.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pvx_17979/08_2025/8pvx_17979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvx_17979/08_2025/8pvx_17979.map" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 110 5.16 5 C 9565 2.51 5 N 2545 2.21 5 O 2905 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15140 Number of models: 1 Model: "" Number of chains: 15 Chain: "H" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 100 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 100 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "E" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 100 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 100 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 100 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.23, per 1000 atoms: 0.21 Number of scatterers: 15140 At special positions: 0 Unit cell: (101.64, 90.75, 189.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 110 16.00 P 10 15.00 Mg 5 11.99 O 2905 8.00 N 2545 7.00 C 9565 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 483.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3550 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 30 sheets defined 53.6% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'H' and resid 2 through 13 Processing helix chain 'C' and resid 55 through 62 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.732A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 180 through 196 removed outlier: 3.847A pdb=" N ASP C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 263 Proline residue: C 258 - end of helix removed outlier: 4.307A pdb=" N LEU C 261 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.584A pdb=" N ARG C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 349 removed outlier: 4.326A pdb=" N VAL C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TRP C 340 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 367 through 374 removed outlier: 4.351A pdb=" N LYS C 373 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 13 Processing helix chain 'E' and resid 55 through 62 removed outlier: 3.511A pdb=" N SER E 60 " --> pdb=" O ASP E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.737A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 180 through 196 removed outlier: 3.853A pdb=" N ASP E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 263 Proline residue: E 258 - end of helix removed outlier: 4.338A pdb=" N LEU E 261 " --> pdb=" O CYS E 257 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE E 262 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 273 through 285 Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.578A pdb=" N ARG E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 349 removed outlier: 3.606A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 356 Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 367 through 372 Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'A' and resid 55 through 62 removed outlier: 3.512A pdb=" N SER A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.710A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.823A pdb=" N ASP A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 263 Proline residue: A 258 - end of helix removed outlier: 4.344A pdb=" N LEU A 261 " --> pdb=" O CYS A 257 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 273 through 285 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.578A pdb=" N ARG A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 349 removed outlier: 4.303A pdb=" N VAL A 339 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N TRP A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 4.218A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 367 through 374 removed outlier: 4.343A pdb=" N LYS A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 13 Processing helix chain 'D' and resid 55 through 62 removed outlier: 3.500A pdb=" N SER D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.771A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.788A pdb=" N ASP D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 263 Proline residue: D 258 - end of helix removed outlier: 4.258A pdb=" N LEU D 261 " --> pdb=" O CYS D 257 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 273 through 285 Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.584A pdb=" N ARG D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 349 removed outlier: 4.301A pdb=" N VAL D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP D 340 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 367 through 374 removed outlier: 4.344A pdb=" N LYS D 373 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 13 Processing helix chain 'B' and resid 55 through 62 removed outlier: 3.524A pdb=" N SER B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.775A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.804A pdb=" N ASP B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 263 Proline residue: B 258 - end of helix removed outlier: 4.291A pdb=" N LEU B 261 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.549A pdb=" N ARG B 290 " --> pdb=" O ASP B 286 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 349 removed outlier: 4.341A pdb=" N VAL B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TRP B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 367 through 374 removed outlier: 4.307A pdb=" N LYS B 373 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 17 through 21 removed outlier: 3.617A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 42 removed outlier: 4.049A pdb=" N GLN C 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 41 through 42 removed outlier: 4.049A pdb=" N GLN C 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 179 removed outlier: 6.104A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 176 through 179 removed outlier: 4.055A pdb=" N GLN A 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'E' and resid 17 through 21 removed outlier: 3.642A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'A' and resid 17 through 21 removed outlier: 3.679A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.192A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 17 through 21 removed outlier: 3.843A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 176 through 179 removed outlier: 6.148A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 176 through 179 removed outlier: 4.078A pdb=" N GLN B 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'B' and resid 17 through 21 removed outlier: 3.704A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.262A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 238 through 241 766 hydrogen bonds defined for protein. 1971 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: 3.16 Time building geometry restraints manager: 1.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4902 1.34 - 1.46: 3036 1.46 - 1.58: 7312 1.58 - 1.70: 15 1.70 - 1.81: 195 Bond restraints: 15460 Sorted by residual: bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.15e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.13e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.11e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.02e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.79e+00 ... (remaining 15455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 20428 2.19 - 4.38: 461 4.38 - 6.58: 53 6.58 - 8.77: 13 8.77 - 10.96: 5 Bond angle restraints: 20960 Sorted by residual: angle pdb=" C1' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C3' ADP C 401 " ideal model delta sigma weight residual 111.00 100.04 10.96 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C1' ADP A 401 " pdb=" C2' ADP A 401 " pdb=" C3' ADP A 401 " ideal model delta sigma weight residual 111.00 100.13 10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" C1' ADP B 401 " pdb=" C2' ADP B 401 " pdb=" C3' ADP B 401 " ideal model delta sigma weight residual 111.00 100.21 10.79 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C1' ADP E 401 " pdb=" C2' ADP E 401 " pdb=" C3' ADP E 401 " ideal model delta sigma weight residual 111.00 100.28 10.72 3.00e+00 1.11e-01 1.28e+01 angle pdb=" C1' ADP D 401 " pdb=" C2' ADP D 401 " pdb=" C3' ADP D 401 " ideal model delta sigma weight residual 111.00 100.52 10.48 3.00e+00 1.11e-01 1.22e+01 ... (remaining 20955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 8928 24.18 - 48.35: 317 48.35 - 72.53: 40 72.53 - 96.70: 15 96.70 - 120.88: 5 Dihedral angle restraints: 9305 sinusoidal: 3765 harmonic: 5540 Sorted by residual: dihedral pdb=" C5' ADP D 401 " pdb=" O5' ADP D 401 " pdb=" PA ADP D 401 " pdb=" O2A ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 60.88 -120.88 1 2.00e+01 2.50e-03 3.63e+01 dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 60.66 -120.66 1 2.00e+01 2.50e-03 3.62e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 60.64 -120.64 1 2.00e+01 2.50e-03 3.62e+01 ... (remaining 9302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1703 0.049 - 0.098: 468 0.098 - 0.148: 144 0.148 - 0.197: 15 0.197 - 0.246: 5 Chirality restraints: 2335 Sorted by residual: chirality pdb=" CA LYS D 61 " pdb=" N LYS D 61 " pdb=" C LYS D 61 " pdb=" CB LYS D 61 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA LYS E 61 " pdb=" N LYS E 61 " pdb=" C LYS E 61 " pdb=" CB LYS E 61 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA LYS A 61 " pdb=" N LYS A 61 " pdb=" C LYS A 61 " pdb=" CB LYS A 61 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 2332 not shown) Planarity restraints: 2670 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 39 " 0.257 9.50e-02 1.11e+02 1.16e-01 1.10e+01 pdb=" NE ARG A 39 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 39 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG A 39 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 39 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 39 " -0.257 9.50e-02 1.11e+02 1.16e-01 1.10e+01 pdb=" NE ARG D 39 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 39 " -0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG D 39 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG D 39 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 39 " 0.257 9.50e-02 1.11e+02 1.16e-01 1.10e+01 pdb=" NE ARG C 39 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG C 39 " 0.026 2.00e-02 2.50e+03 pdb=" NH1 ARG C 39 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG C 39 " -0.000 2.00e-02 2.50e+03 ... (remaining 2667 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 100 2.54 - 3.13: 12328 3.13 - 3.72: 23592 3.72 - 4.31: 33973 4.31 - 4.90: 55462 Nonbonded interactions: 125455 Sorted by model distance: nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 1.951 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 1.955 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 1.992 2.170 nonbonded pdb=" O1A ADP D 401 " pdb="MG MG D 402 " model vdw 2.038 2.170 nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 2.053 2.170 ... (remaining 125450 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.730 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 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 : 0.003 0.057 15460 Z= 0.169 Angle : 0.795 10.962 20960 Z= 0.438 Chirality : 0.050 0.246 2335 Planarity : 0.009 0.116 2670 Dihedral : 13.294 120.875 5755 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.18), residues: 1885 helix: -0.59 (0.15), residues: 825 sheet: 0.61 (0.27), residues: 310 loop : 0.17 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.004 ARG A 39 TYR 0.028 0.005 TYR A 306 PHE 0.017 0.002 PHE B 255 TRP 0.031 0.005 TRP E 356 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00333 (15460) covalent geometry : angle 0.79495 (20960) hydrogen bonds : bond 0.15795 ( 751) hydrogen bonds : angle 7.13173 ( 1971) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.394 Fit side-chains REVERT: H 1 MET cc_start: 0.6956 (tpp) cc_final: 0.6671 (tpt) REVERT: C 227 MET cc_start: 0.8941 (mmm) cc_final: 0.8687 (mmm) REVERT: C 283 MET cc_start: 0.9145 (mmp) cc_final: 0.8918 (mmp) REVERT: C 313 MET cc_start: 0.9083 (mmm) cc_final: 0.8713 (tpt) REVERT: E 283 MET cc_start: 0.9292 (mmp) cc_final: 0.9056 (mmm) REVERT: E 305 MET cc_start: 0.9223 (mmm) cc_final: 0.8723 (mmt) REVERT: A 176 MET cc_start: 0.7776 (mtt) cc_final: 0.7539 (mtt) REVERT: A 305 MET cc_start: 0.8943 (mmm) cc_final: 0.8686 (mmt) REVERT: A 355 MET cc_start: 0.8911 (mmm) cc_final: 0.8668 (mmp) REVERT: D 313 MET cc_start: 0.9457 (mmm) cc_final: 0.9149 (tpt) REVERT: D 355 MET cc_start: 0.8878 (mmm) cc_final: 0.8628 (mmp) REVERT: G 5 ASP cc_start: 0.8751 (m-30) cc_final: 0.8474 (t0) REVERT: B 355 MET cc_start: 0.8659 (mmm) cc_final: 0.8137 (mmm) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1148 time to fit residues: 21.9073 Evaluate side-chains 111 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.0020 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 overall best weight: 0.5770 ------------------------------------------------------------------------------- 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 = 0.2972 r_free = 0.2972 target = 0.036180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.030481 restraints weight = 101854.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.031735 restraints weight = 47940.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.032608 restraints weight = 28827.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.033220 restraints weight = 19739.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.033648 restraints weight = 14753.345| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15460 Z= 0.116 Angle : 0.617 8.199 20960 Z= 0.304 Chirality : 0.044 0.174 2335 Planarity : 0.005 0.070 2670 Dihedral : 8.351 89.226 2145 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.37 % Allowed : 2.16 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.19), residues: 1885 helix: 0.65 (0.17), residues: 845 sheet: 1.13 (0.29), residues: 280 loop : 0.56 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 290 TYR 0.022 0.002 TYR C 306 PHE 0.017 0.001 PHE D 375 TRP 0.021 0.003 TRP A 86 HIS 0.002 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00239 (15460) covalent geometry : angle 0.61714 (20960) hydrogen bonds : bond 0.03631 ( 751) hydrogen bonds : angle 5.21255 ( 1971) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 117 time to evaluate : 0.628 Fit side-chains REVERT: C 176 MET cc_start: 0.8827 (mtt) cc_final: 0.8626 (mtt) REVERT: C 227 MET cc_start: 0.8934 (mmm) cc_final: 0.8621 (mmm) REVERT: C 269 MET cc_start: 0.9051 (mtm) cc_final: 0.8689 (mtp) REVERT: C 313 MET cc_start: 0.9156 (mmm) cc_final: 0.8789 (tpt) REVERT: E 269 MET cc_start: 0.9009 (mtm) cc_final: 0.8785 (mtm) REVERT: E 305 MET cc_start: 0.9429 (mmm) cc_final: 0.9156 (mmt) REVERT: A 283 MET cc_start: 0.9415 (mmm) cc_final: 0.9151 (mmm) REVERT: A 299 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8587 (mtp) REVERT: A 305 MET cc_start: 0.9102 (mmm) cc_final: 0.8814 (tpp) REVERT: A 355 MET cc_start: 0.8955 (mmm) cc_final: 0.8648 (mmm) REVERT: D 313 MET cc_start: 0.9366 (mmm) cc_final: 0.9070 (tpp) REVERT: B 47 MET cc_start: 0.7036 (mmm) cc_final: 0.6816 (mmm) outliers start: 6 outliers final: 1 residues processed: 118 average time/residue: 0.1173 time to fit residues: 21.4100 Evaluate side-chains 113 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain A residue 299 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 119 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 171 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.032603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.027014 restraints weight = 105131.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.028104 restraints weight = 52281.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.028912 restraints weight = 32643.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.029466 restraints weight = 22969.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.029855 restraints weight = 17645.357| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 15460 Z= 0.340 Angle : 0.722 7.072 20960 Z= 0.358 Chirality : 0.049 0.172 2335 Planarity : 0.005 0.062 2670 Dihedral : 8.118 85.777 2145 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.19 % Allowed : 4.07 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.19), residues: 1885 helix: 0.58 (0.18), residues: 850 sheet: 0.75 (0.29), residues: 280 loop : 0.50 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 335 TYR 0.013 0.002 TYR E 279 PHE 0.021 0.002 PHE B 262 TRP 0.018 0.003 TRP A 356 HIS 0.011 0.002 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00758 (15460) covalent geometry : angle 0.72186 (20960) hydrogen bonds : bond 0.04517 ( 751) hydrogen bonds : angle 5.46199 ( 1971) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.365 Fit side-chains REVERT: C 269 MET cc_start: 0.9081 (mtm) cc_final: 0.8851 (mtp) REVERT: C 313 MET cc_start: 0.9317 (mmm) cc_final: 0.8777 (tpt) REVERT: C 325 MET cc_start: 0.7993 (ttm) cc_final: 0.7449 (ttm) REVERT: E 305 MET cc_start: 0.9328 (mmm) cc_final: 0.8790 (mmt) REVERT: A 305 MET cc_start: 0.9223 (mmm) cc_final: 0.8948 (tpp) REVERT: D 227 MET cc_start: 0.9320 (mmt) cc_final: 0.8674 (tpp) REVERT: D 313 MET cc_start: 0.9512 (mmm) cc_final: 0.8715 (tpt) REVERT: B 269 MET cc_start: 0.9198 (mtp) cc_final: 0.8969 (mtp) REVERT: B 325 MET cc_start: 0.5869 (ttm) cc_final: 0.5536 (ttm) outliers start: 3 outliers final: 1 residues processed: 112 average time/residue: 0.1174 time to fit residues: 20.2103 Evaluate side-chains 110 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 127 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.2910 r_free = 0.2910 target = 0.034428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.028845 restraints weight = 101031.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.029968 restraints weight = 49396.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.030798 restraints weight = 30407.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.031361 restraints weight = 21252.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.031743 restraints weight = 16199.959| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15460 Z= 0.102 Angle : 0.560 7.588 20960 Z= 0.269 Chirality : 0.042 0.142 2335 Planarity : 0.004 0.060 2670 Dihedral : 7.360 80.672 2145 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.19 % Allowed : 4.75 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.20), residues: 1885 helix: 1.15 (0.18), residues: 805 sheet: 0.77 (0.30), residues: 280 loop : 0.83 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 290 TYR 0.018 0.001 TYR D 306 PHE 0.008 0.001 PHE D 255 TRP 0.012 0.002 TRP E 356 HIS 0.004 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00222 (15460) covalent geometry : angle 0.55989 (20960) hydrogen bonds : bond 0.03148 ( 751) hydrogen bonds : angle 4.78373 ( 1971) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.636 Fit side-chains REVERT: C 305 MET cc_start: 0.9057 (mmm) cc_final: 0.8692 (mmt) REVERT: C 313 MET cc_start: 0.9250 (mmm) cc_final: 0.8770 (tpt) REVERT: C 325 MET cc_start: 0.7780 (ttm) cc_final: 0.7329 (ttm) REVERT: E 132 MET cc_start: 0.8298 (tmm) cc_final: 0.8014 (tmm) REVERT: E 305 MET cc_start: 0.9426 (mmm) cc_final: 0.8906 (mmt) REVERT: E 358 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.7868 (p) REVERT: A 176 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.8052 (mtt) REVERT: A 305 MET cc_start: 0.9111 (mmm) cc_final: 0.8857 (tpp) REVERT: D 227 MET cc_start: 0.9298 (mmt) cc_final: 0.8651 (mpp) REVERT: D 269 MET cc_start: 0.8846 (mtp) cc_final: 0.8624 (mtp) REVERT: D 305 MET cc_start: 0.9096 (tpp) cc_final: 0.8677 (mmm) REVERT: D 313 MET cc_start: 0.9431 (mmm) cc_final: 0.9115 (tpp) REVERT: B 325 MET cc_start: 0.5701 (ttm) cc_final: 0.5356 (ttm) outliers start: 3 outliers final: 1 residues processed: 117 average time/residue: 0.1100 time to fit residues: 20.3913 Evaluate side-chains 116 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain A residue 176 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 170 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 152 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.2895 r_free = 0.2895 target = 0.034034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.028423 restraints weight = 102567.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.029549 restraints weight = 50431.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.030371 restraints weight = 31210.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.030939 restraints weight = 21831.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.031348 restraints weight = 16662.718| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15460 Z= 0.129 Angle : 0.557 9.700 20960 Z= 0.264 Chirality : 0.043 0.139 2335 Planarity : 0.004 0.059 2670 Dihedral : 7.141 84.368 2145 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.31 % Allowed : 5.74 % Favored : 93.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.20), residues: 1885 helix: 1.48 (0.19), residues: 775 sheet: 0.63 (0.30), residues: 280 loop : 0.96 (0.24), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 290 TYR 0.011 0.001 TYR A 306 PHE 0.015 0.001 PHE B 375 TRP 0.011 0.002 TRP B 79 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00291 (15460) covalent geometry : angle 0.55699 (20960) hydrogen bonds : bond 0.03119 ( 751) hydrogen bonds : angle 4.73222 ( 1971) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.619 Fit side-chains REVERT: C 313 MET cc_start: 0.9317 (mmm) cc_final: 0.8793 (tpt) REVERT: E 305 MET cc_start: 0.9422 (mmm) cc_final: 0.8894 (mmt) REVERT: E 358 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8063 (t) REVERT: A 44 MET cc_start: 0.8951 (mmm) cc_final: 0.8724 (mmm) REVERT: A 227 MET cc_start: 0.9287 (mmm) cc_final: 0.8873 (mmm) REVERT: A 305 MET cc_start: 0.9167 (mmm) cc_final: 0.8891 (tpp) REVERT: D 227 MET cc_start: 0.9321 (mmt) cc_final: 0.8700 (tpp) REVERT: D 313 MET cc_start: 0.9453 (mmm) cc_final: 0.9045 (tpp) REVERT: B 227 MET cc_start: 0.8797 (mmm) cc_final: 0.8074 (mpp) REVERT: B 313 MET cc_start: 0.9447 (tpp) cc_final: 0.9232 (mmt) outliers start: 5 outliers final: 2 residues processed: 116 average time/residue: 0.1226 time to fit residues: 22.3246 Evaluate side-chains 114 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain B residue 47 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 154 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 136 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 103 optimal weight: 0.0040 chunk 92 optimal weight: 10.0000 chunk 141 optimal weight: 0.0970 chunk 32 optimal weight: 9.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- 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 = 0.2914 r_free = 0.2914 target = 0.034466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.028881 restraints weight = 101498.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.030021 restraints weight = 49809.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.030844 restraints weight = 30703.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.031409 restraints weight = 21426.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.031816 restraints weight = 16360.426| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15460 Z= 0.103 Angle : 0.545 9.179 20960 Z= 0.255 Chirality : 0.042 0.138 2335 Planarity : 0.004 0.060 2670 Dihedral : 6.892 77.989 2145 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.37 % Allowed : 6.73 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.20), residues: 1885 helix: 1.32 (0.18), residues: 815 sheet: 0.59 (0.30), residues: 280 loop : 1.01 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 256 TYR 0.013 0.001 TYR D 306 PHE 0.011 0.001 PHE B 375 TRP 0.010 0.001 TRP D 356 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00233 (15460) covalent geometry : angle 0.54481 (20960) hydrogen bonds : bond 0.02872 ( 751) hydrogen bonds : angle 4.58463 ( 1971) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.705 Fit side-chains REVERT: H 5 ASP cc_start: 0.9264 (m-30) cc_final: 0.8977 (t70) REVERT: C 313 MET cc_start: 0.9320 (mmm) cc_final: 0.8790 (tpt) REVERT: C 325 MET cc_start: 0.7880 (ttp) cc_final: 0.7583 (ttm) REVERT: E 132 MET cc_start: 0.8377 (tmm) cc_final: 0.8131 (tmm) REVERT: E 305 MET cc_start: 0.9433 (mmm) cc_final: 0.8898 (mmt) REVERT: E 358 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8147 (t) REVERT: F 9 LYS cc_start: 0.8914 (pttt) cc_final: 0.8482 (pptt) REVERT: A 283 MET cc_start: 0.9410 (mmm) cc_final: 0.9209 (mmm) REVERT: A 299 MET cc_start: 0.8618 (mmm) cc_final: 0.8369 (mtp) REVERT: A 305 MET cc_start: 0.9147 (mmm) cc_final: 0.8861 (tpp) REVERT: D 283 MET cc_start: 0.9099 (mmm) cc_final: 0.8874 (mmm) REVERT: D 305 MET cc_start: 0.9047 (tpp) cc_final: 0.8680 (mmm) REVERT: D 313 MET cc_start: 0.9464 (mmm) cc_final: 0.9077 (tpp) REVERT: G 7 ILE cc_start: 0.8349 (tt) cc_final: 0.8121 (tt) REVERT: B 227 MET cc_start: 0.8808 (mmm) cc_final: 0.8044 (mpp) REVERT: B 313 MET cc_start: 0.9411 (tpp) cc_final: 0.9177 (mmt) REVERT: B 325 MET cc_start: 0.6153 (ttm) cc_final: 0.5859 (ttm) outliers start: 6 outliers final: 3 residues processed: 113 average time/residue: 0.1167 time to fit residues: 20.6420 Evaluate side-chains 114 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain B residue 47 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 51 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.033144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.027580 restraints weight = 103011.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.028683 restraints weight = 51162.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.029486 restraints weight = 31913.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.030037 restraints weight = 22447.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.030430 restraints weight = 17186.578| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 15460 Z= 0.220 Angle : 0.606 7.110 20960 Z= 0.289 Chirality : 0.044 0.147 2335 Planarity : 0.004 0.056 2670 Dihedral : 7.079 79.447 2145 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.31 % Allowed : 7.16 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.20), residues: 1885 helix: 1.30 (0.19), residues: 805 sheet: 0.45 (0.30), residues: 280 loop : 0.91 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 256 TYR 0.010 0.001 TYR E 279 PHE 0.012 0.001 PHE B 375 TRP 0.012 0.002 TRP C 79 HIS 0.005 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00491 (15460) covalent geometry : angle 0.60561 (20960) hydrogen bonds : bond 0.03469 ( 751) hydrogen bonds : angle 4.83545 ( 1971) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.616 Fit side-chains REVERT: H 5 ASP cc_start: 0.9295 (m-30) cc_final: 0.9030 (t70) REVERT: E 132 MET cc_start: 0.8333 (tmm) cc_final: 0.8031 (tmm) REVERT: E 305 MET cc_start: 0.9389 (mmm) cc_final: 0.8860 (mmt) REVERT: E 358 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8241 (t) REVERT: F 9 LYS cc_start: 0.8812 (pttt) cc_final: 0.8593 (ptmt) REVERT: A 227 MET cc_start: 0.9228 (mmm) cc_final: 0.8798 (mmm) REVERT: A 305 MET cc_start: 0.9217 (mmm) cc_final: 0.8905 (tpp) REVERT: D 305 MET cc_start: 0.9123 (tpp) cc_final: 0.8644 (mmm) REVERT: D 313 MET cc_start: 0.9520 (mmm) cc_final: 0.9098 (tpp) REVERT: B 227 MET cc_start: 0.8859 (mmm) cc_final: 0.8085 (mpp) REVERT: B 313 MET cc_start: 0.9432 (tpp) cc_final: 0.9205 (mmt) outliers start: 5 outliers final: 3 residues processed: 109 average time/residue: 0.1277 time to fit residues: 21.5489 Evaluate side-chains 111 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain J residue 7 ILE Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain B residue 47 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 166 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.2868 r_free = 0.2868 target = 0.033394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.027814 restraints weight = 103128.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.028927 restraints weight = 51137.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.029737 restraints weight = 31762.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.030296 restraints weight = 22271.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.030692 restraints weight = 17011.927| |-----------------------------------------------------------------------------| r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15460 Z= 0.174 Angle : 0.581 7.788 20960 Z= 0.274 Chirality : 0.044 0.136 2335 Planarity : 0.004 0.056 2670 Dihedral : 6.987 78.199 2145 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.31 % Allowed : 7.47 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.20), residues: 1885 helix: 1.57 (0.19), residues: 775 sheet: 0.37 (0.30), residues: 280 loop : 0.96 (0.24), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 256 TYR 0.010 0.001 TYR A 306 PHE 0.011 0.001 PHE B 375 TRP 0.011 0.002 TRP E 79 HIS 0.003 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00392 (15460) covalent geometry : angle 0.58067 (20960) hydrogen bonds : bond 0.03208 ( 751) hydrogen bonds : angle 4.76385 ( 1971) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.539 Fit side-chains REVERT: H 5 ASP cc_start: 0.9265 (m-30) cc_final: 0.9037 (t70) REVERT: C 305 MET cc_start: 0.8743 (mmt) cc_final: 0.8485 (mmm) REVERT: C 313 MET cc_start: 0.9417 (mmm) cc_final: 0.8846 (tpt) REVERT: E 132 MET cc_start: 0.8374 (tmm) cc_final: 0.7929 (tmm) REVERT: E 305 MET cc_start: 0.9387 (mmm) cc_final: 0.8826 (mmt) REVERT: E 358 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8247 (t) REVERT: F 9 LYS cc_start: 0.8999 (pttt) cc_final: 0.8794 (ptmt) REVERT: A 227 MET cc_start: 0.9218 (mmm) cc_final: 0.8857 (mmm) REVERT: A 305 MET cc_start: 0.9215 (mmm) cc_final: 0.8910 (tpp) REVERT: D 227 MET cc_start: 0.9253 (tpp) cc_final: 0.8637 (mpp) REVERT: D 283 MET cc_start: 0.9133 (mmm) cc_final: 0.8862 (mmm) REVERT: D 305 MET cc_start: 0.9127 (tpp) cc_final: 0.8695 (mmm) REVERT: D 313 MET cc_start: 0.9492 (mmm) cc_final: 0.9110 (tpp) REVERT: B 227 MET cc_start: 0.8837 (mmm) cc_final: 0.8213 (tpp) outliers start: 5 outliers final: 2 residues processed: 111 average time/residue: 0.1159 time to fit residues: 20.0426 Evaluate side-chains 110 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain B residue 47 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.2904 r_free = 0.2904 target = 0.034222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.028628 restraints weight = 101796.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.029767 restraints weight = 50249.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.030578 restraints weight = 31073.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.031138 restraints weight = 21795.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.031547 restraints weight = 16678.787| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15460 Z= 0.098 Angle : 0.557 11.892 20960 Z= 0.259 Chirality : 0.043 0.137 2335 Planarity : 0.004 0.056 2670 Dihedral : 6.772 77.384 2145 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.31 % Allowed : 7.84 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.20), residues: 1885 helix: 1.47 (0.19), residues: 805 sheet: 0.39 (0.30), residues: 280 loop : 1.01 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.012 0.001 TYR D 306 PHE 0.010 0.001 PHE B 375 TRP 0.013 0.002 TRP D 356 HIS 0.003 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00222 (15460) covalent geometry : angle 0.55719 (20960) hydrogen bonds : bond 0.02840 ( 751) hydrogen bonds : angle 4.59259 ( 1971) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.570 Fit side-chains REVERT: C 305 MET cc_start: 0.8769 (mmt) cc_final: 0.8491 (mmm) REVERT: C 313 MET cc_start: 0.9360 (mmm) cc_final: 0.8797 (tpt) REVERT: E 132 MET cc_start: 0.8378 (tmm) cc_final: 0.8006 (tmm) REVERT: E 305 MET cc_start: 0.9407 (mmm) cc_final: 0.8868 (mmt) REVERT: E 358 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8232 (t) REVERT: F 9 LYS cc_start: 0.9014 (pttt) cc_final: 0.8785 (ptmt) REVERT: A 283 MET cc_start: 0.9369 (mmm) cc_final: 0.9147 (mmm) REVERT: A 299 MET cc_start: 0.8634 (mmm) cc_final: 0.8404 (mtp) REVERT: A 305 MET cc_start: 0.9138 (mmm) cc_final: 0.8809 (tpp) REVERT: D 227 MET cc_start: 0.9180 (tpp) cc_final: 0.8857 (tpp) REVERT: D 283 MET cc_start: 0.9160 (mmm) cc_final: 0.8904 (mmm) REVERT: D 305 MET cc_start: 0.9053 (tpp) cc_final: 0.8663 (mmm) REVERT: D 313 MET cc_start: 0.9472 (mmm) cc_final: 0.9150 (tpp) REVERT: B 227 MET cc_start: 0.8819 (mmm) cc_final: 0.8188 (tpp) REVERT: B 325 MET cc_start: 0.5948 (ttm) cc_final: 0.5633 (ttm) outliers start: 5 outliers final: 2 residues processed: 111 average time/residue: 0.1276 time to fit residues: 21.9049 Evaluate side-chains 110 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain B residue 47 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 44 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.2874 r_free = 0.2874 target = 0.033498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.027872 restraints weight = 103314.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.028999 restraints weight = 51379.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.029810 restraints weight = 31897.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.030371 restraints weight = 22374.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.030774 restraints weight = 17118.589| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15460 Z= 0.178 Angle : 0.593 11.148 20960 Z= 0.278 Chirality : 0.044 0.139 2335 Planarity : 0.004 0.054 2670 Dihedral : 6.830 77.720 2145 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.19 % Allowed : 7.84 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.20), residues: 1885 helix: 1.16 (0.18), residues: 845 sheet: 0.37 (0.30), residues: 280 loop : 0.88 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 335 TYR 0.008 0.001 TYR A 306 PHE 0.010 0.001 PHE B 375 TRP 0.010 0.001 TRP C 79 HIS 0.004 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00401 (15460) covalent geometry : angle 0.59266 (20960) hydrogen bonds : bond 0.03172 ( 751) hydrogen bonds : angle 4.71641 ( 1971) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.528 Fit side-chains REVERT: C 123 MET cc_start: 0.9145 (tpp) cc_final: 0.8827 (tpp) REVERT: C 325 MET cc_start: 0.7739 (ttp) cc_final: 0.7377 (ttm) REVERT: E 132 MET cc_start: 0.8469 (tmm) cc_final: 0.8046 (tmm) REVERT: E 305 MET cc_start: 0.9382 (mmm) cc_final: 0.8825 (mmt) REVERT: E 358 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8255 (t) REVERT: F 9 LYS cc_start: 0.9011 (pttt) cc_final: 0.8757 (ptmt) REVERT: A 227 MET cc_start: 0.9203 (mmm) cc_final: 0.8809 (mmm) REVERT: A 283 MET cc_start: 0.9346 (mmm) cc_final: 0.9101 (mmm) REVERT: A 305 MET cc_start: 0.9177 (mmm) cc_final: 0.8849 (tpp) REVERT: D 227 MET cc_start: 0.9176 (tpp) cc_final: 0.8827 (tpp) REVERT: D 283 MET cc_start: 0.9121 (mmm) cc_final: 0.8848 (mmm) REVERT: D 305 MET cc_start: 0.9090 (tpp) cc_final: 0.8691 (mmm) REVERT: D 313 MET cc_start: 0.9513 (mmm) cc_final: 0.9105 (tpp) REVERT: B 227 MET cc_start: 0.8849 (mmm) cc_final: 0.8212 (tpp) outliers start: 3 outliers final: 2 residues processed: 108 average time/residue: 0.1215 time to fit residues: 20.4270 Evaluate side-chains 109 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain B residue 47 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 9.9990 chunk 170 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN E 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.032693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.026957 restraints weight = 103061.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.028095 restraints weight = 50581.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.028900 restraints weight = 31299.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.029452 restraints weight = 22037.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.029846 restraints weight = 16914.110| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 15460 Z= 0.251 Angle : 0.647 10.769 20960 Z= 0.307 Chirality : 0.045 0.147 2335 Planarity : 0.004 0.053 2670 Dihedral : 7.069 80.003 2145 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.31 % Allowed : 8.02 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.20), residues: 1885 helix: 1.19 (0.19), residues: 815 sheet: 0.25 (0.30), residues: 280 loop : 0.83 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 335 TYR 0.010 0.001 TYR E 279 PHE 0.012 0.001 PHE B 262 TRP 0.011 0.002 TRP C 79 HIS 0.006 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00562 (15460) covalent geometry : angle 0.64689 (20960) hydrogen bonds : bond 0.03631 ( 751) hydrogen bonds : angle 4.96480 ( 1971) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1886.54 seconds wall clock time: 33 minutes 50.51 seconds (2030.51 seconds total)