Starting phenix.real_space_refine on Mon Jan 20 14:19:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvx_17979/01_2025/8pvx_17979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvx_17979/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8pvx_17979/01_2025/8pvx_17979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvx_17979/01_2025/8pvx_17979.map" model { file = "/net/cci-nas-00/data/ceres_data/8pvx_17979/01_2025/8pvx_17979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvx_17979/01_2025/8pvx_17979.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 9.32, per 1000 atoms: 0.62 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: 4.17 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.06 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: 5.47 Time building geometry restraints manager: 4.74 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: 0.06 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 36.650 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.220 ------------------------------------------------------------------------------- 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= 0.225 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), 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 TRP 0.031 0.005 TRP E 356 HIS 0.004 0.001 HIS B 101 PHE 0.017 0.002 PHE B 255 TYR 0.028 0.005 TYR A 306 ARG 0.029 0.004 ARG A 39 *********************** 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 : 1.902 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: 0.2834 time to fit residues: 54.2174 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 : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 chunk 79 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 76 optimal weight: 20.0000 chunk 148 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.2931 r_free = 0.2931 target = 0.035158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.029510 restraints weight = 101901.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.030728 restraints weight = 47953.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.031580 restraints weight = 28923.923| |-----------------------------------------------------------------------------| r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15460 Z= 0.201 Angle : 0.628 8.151 20960 Z= 0.309 Chirality : 0.045 0.187 2335 Planarity : 0.005 0.070 2670 Dihedral : 8.467 89.956 2145 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.31 % Allowed : 2.47 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 1885 helix: 0.62 (0.17), residues: 845 sheet: 1.08 (0.29), residues: 280 loop : 0.52 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 86 HIS 0.003 0.001 HIS D 88 PHE 0.019 0.001 PHE D 375 TYR 0.019 0.002 TYR A 306 ARG 0.006 0.001 ARG A 290 *********************** 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 120 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 1.883 Fit side-chains REVERT: C 227 MET cc_start: 0.8923 (mmm) cc_final: 0.8626 (mmm) REVERT: C 269 MET cc_start: 0.9113 (mtm) cc_final: 0.8721 (mtp) REVERT: C 313 MET cc_start: 0.9207 (mmm) cc_final: 0.8787 (tpt) REVERT: C 325 MET cc_start: 0.7975 (ttp) cc_final: 0.7586 (ttm) REVERT: J 7 ILE cc_start: 0.8839 (mt) cc_final: 0.8637 (mm) REVERT: E 123 MET cc_start: 0.9214 (mmt) cc_final: 0.8792 (mmp) REVERT: E 132 MET cc_start: 0.8218 (tmm) cc_final: 0.8009 (tmm) REVERT: E 283 MET cc_start: 0.9312 (mmp) cc_final: 0.9074 (mmm) REVERT: E 305 MET cc_start: 0.9410 (mmm) cc_final: 0.9139 (mmt) REVERT: A 283 MET cc_start: 0.9418 (mmm) cc_final: 0.9151 (mmm) REVERT: A 305 MET cc_start: 0.9132 (mmm) cc_final: 0.8858 (tpp) REVERT: A 355 MET cc_start: 0.9009 (mmm) cc_final: 0.8731 (mmp) REVERT: D 313 MET cc_start: 0.9387 (mmm) cc_final: 0.8645 (tpt) REVERT: G 5 ASP cc_start: 0.8640 (m-30) cc_final: 0.8402 (t0) REVERT: B 47 MET cc_start: 0.7209 (mmm) cc_final: 0.6964 (mmm) outliers start: 5 outliers final: 1 residues processed: 116 average time/residue: 0.2711 time to fit residues: 48.5828 Evaluate side-chains 114 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 1.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 52 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 = 0.2848 r_free = 0.2848 target = 0.033089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.027389 restraints weight = 103299.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.028555 restraints weight = 49797.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.029370 restraints weight = 30659.344| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 15460 Z= 0.386 Angle : 0.656 6.902 20960 Z= 0.323 Chirality : 0.046 0.163 2335 Planarity : 0.005 0.064 2670 Dihedral : 7.973 84.855 2145 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.19 % Allowed : 3.64 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.19), residues: 1885 helix: 0.67 (0.18), residues: 865 sheet: 0.79 (0.29), residues: 280 loop : 0.33 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 356 HIS 0.008 0.002 HIS D 88 PHE 0.015 0.002 PHE B 262 TYR 0.012 0.001 TYR A 306 ARG 0.005 0.001 ARG D 335 *********************** 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 116 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 1.773 Fit side-chains REVERT: C 176 MET cc_start: 0.8920 (mtt) cc_final: 0.8655 (mtt) REVERT: C 269 MET cc_start: 0.9132 (mtm) cc_final: 0.8894 (mtp) REVERT: C 313 MET cc_start: 0.9314 (mmm) cc_final: 0.8755 (tpt) REVERT: E 123 MET cc_start: 0.9207 (mmt) cc_final: 0.8862 (mmp) REVERT: E 283 MET cc_start: 0.9303 (mmp) cc_final: 0.9086 (mmm) REVERT: E 305 MET cc_start: 0.9379 (mmm) cc_final: 0.8837 (mmt) REVERT: A 44 MET cc_start: 0.8965 (mmm) cc_final: 0.8703 (mmm) REVERT: A 305 MET cc_start: 0.9241 (mmm) cc_final: 0.8962 (tpp) REVERT: A 355 MET cc_start: 0.8981 (mmm) cc_final: 0.8625 (mmm) REVERT: D 227 MET cc_start: 0.9257 (mmt) cc_final: 0.9057 (mmm) REVERT: D 313 MET cc_start: 0.9450 (mmm) cc_final: 0.8636 (tpt) REVERT: G 5 ASP cc_start: 0.8644 (m-30) cc_final: 0.8354 (t0) outliers start: 3 outliers final: 1 residues processed: 114 average time/residue: 0.2734 time to fit residues: 47.8260 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 : 1.722 ------------------------------------------------------------------------------- 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 159 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 185 optimal weight: 0.0170 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- 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 = 0.2867 r_free = 0.2867 target = 0.033556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.027795 restraints weight = 102790.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.028991 restraints weight = 49433.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.029804 restraints weight = 30324.118| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2558 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= 0.243 Angle : 0.581 9.133 20960 Z= 0.279 Chirality : 0.044 0.140 2335 Planarity : 0.004 0.062 2670 Dihedral : 7.332 78.578 2145 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.06 % Allowed : 4.81 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.20), residues: 1885 helix: 0.91 (0.18), residues: 835 sheet: 0.66 (0.29), residues: 280 loop : 0.80 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 356 HIS 0.004 0.001 HIS D 88 PHE 0.009 0.001 PHE B 262 TYR 0.015 0.001 TYR D 306 ARG 0.003 0.000 ARG A 335 *********************** 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 114 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 1.822 Fit side-chains REVERT: C 176 MET cc_start: 0.8932 (mtt) cc_final: 0.8719 (mtt) REVERT: C 305 MET cc_start: 0.9160 (mmm) cc_final: 0.8683 (mmt) REVERT: C 313 MET cc_start: 0.9344 (mmm) cc_final: 0.8819 (tpt) REVERT: C 325 MET cc_start: 0.8081 (ttp) cc_final: 0.7607 (ttm) REVERT: E 123 MET cc_start: 0.9244 (mmt) cc_final: 0.8805 (mmp) REVERT: E 305 MET cc_start: 0.9455 (mmm) cc_final: 0.8912 (mmt) REVERT: A 44 MET cc_start: 0.9052 (mmm) cc_final: 0.8749 (mmm) REVERT: A 305 MET cc_start: 0.9187 (mmm) cc_final: 0.8919 (tpp) REVERT: A 355 MET cc_start: 0.8977 (mmm) cc_final: 0.8678 (mmm) REVERT: D 227 MET cc_start: 0.9251 (mmt) cc_final: 0.8620 (tpp) REVERT: D 305 MET cc_start: 0.9127 (tpp) cc_final: 0.8608 (mmm) REVERT: D 313 MET cc_start: 0.9437 (mmm) cc_final: 0.9042 (tpp) REVERT: G 5 ASP cc_start: 0.8705 (m-30) cc_final: 0.8394 (t0) outliers start: 1 outliers final: 1 residues processed: 114 average time/residue: 0.2677 time to fit residues: 47.1103 Evaluate side-chains 113 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 146 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 0.0870 chunk 29 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.032796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.027052 restraints weight = 104620.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.028213 restraints weight = 50756.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.029027 restraints weight = 31153.322| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 15460 Z= 0.343 Angle : 0.621 7.391 20960 Z= 0.300 Chirality : 0.045 0.152 2335 Planarity : 0.004 0.059 2670 Dihedral : 7.332 78.815 2145 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.31 % Allowed : 6.17 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1885 helix: 1.16 (0.19), residues: 805 sheet: 0.40 (0.29), residues: 280 loop : 0.81 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.006 0.001 HIS D 88 PHE 0.013 0.001 PHE B 262 TYR 0.009 0.001 TYR A 306 ARG 0.004 0.000 ARG A 335 *********************** 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 114 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 109 time to evaluate : 1.975 Fit side-chains revert: symmetry clash REVERT: H 5 ASP cc_start: 0.9300 (m-30) cc_final: 0.8950 (t70) REVERT: C 305 MET cc_start: 0.9183 (mmm) cc_final: 0.8939 (tpp) REVERT: C 325 MET cc_start: 0.8233 (ttp) cc_final: 0.7987 (ttm) REVERT: E 123 MET cc_start: 0.9243 (mmt) cc_final: 0.8891 (mmp) REVERT: E 132 MET cc_start: 0.8429 (tmm) cc_final: 0.8150 (tmm) REVERT: E 227 MET cc_start: 0.9122 (mmm) cc_final: 0.8919 (tpt) REVERT: E 305 MET cc_start: 0.9431 (mmm) cc_final: 0.8879 (mmt) REVERT: E 358 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.7992 (t) REVERT: A 44 MET cc_start: 0.9079 (mmm) cc_final: 0.8753 (mmm) REVERT: A 305 MET cc_start: 0.9274 (mmm) cc_final: 0.8987 (tpp) REVERT: A 355 MET cc_start: 0.9001 (mmm) cc_final: 0.8722 (mmm) REVERT: D 227 MET cc_start: 0.9266 (mmt) cc_final: 0.8603 (tpp) REVERT: D 313 MET cc_start: 0.9480 (mmm) cc_final: 0.9082 (tpp) REVERT: G 5 ASP cc_start: 0.8784 (m-30) cc_final: 0.8378 (t0) REVERT: B 227 MET cc_start: 0.8760 (mmm) cc_final: 0.8063 (mpp) outliers start: 5 outliers final: 1 residues processed: 111 average time/residue: 0.2634 time to fit residues: 45.7227 Evaluate side-chains 111 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 103 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 GLN ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.032449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.026748 restraints weight = 104464.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.027878 restraints weight = 50726.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.028689 restraints weight = 31319.941| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 15460 Z= 0.399 Angle : 0.645 9.766 20960 Z= 0.313 Chirality : 0.046 0.146 2335 Planarity : 0.004 0.057 2670 Dihedral : 7.349 78.604 2145 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.49 % Allowed : 6.79 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.20), residues: 1885 helix: 1.09 (0.19), residues: 805 sheet: 0.24 (0.29), residues: 280 loop : 0.70 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.006 0.001 HIS D 88 PHE 0.013 0.002 PHE B 262 TYR 0.011 0.001 TYR E 279 ARG 0.004 0.001 ARG D 335 *********************** 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 118 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.804 Fit side-chains REVERT: H 5 ASP cc_start: 0.9329 (m-30) cc_final: 0.8996 (t70) REVERT: C 123 MET cc_start: 0.9233 (tpp) cc_final: 0.8929 (tpp) REVERT: C 176 MET cc_start: 0.8862 (mtt) cc_final: 0.8641 (mtt) REVERT: C 305 MET cc_start: 0.9126 (mmm) cc_final: 0.8883 (tpp) REVERT: C 325 MET cc_start: 0.8327 (ttp) cc_final: 0.8085 (ttm) REVERT: E 123 MET cc_start: 0.9190 (mmt) cc_final: 0.8741 (mmp) REVERT: E 227 MET cc_start: 0.9122 (mmm) cc_final: 0.8899 (tpt) REVERT: E 305 MET cc_start: 0.9411 (mmm) cc_final: 0.8854 (mmt) REVERT: E 358 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8061 (t) REVERT: A 44 MET cc_start: 0.9102 (mmm) cc_final: 0.8753 (mmm) REVERT: A 227 MET cc_start: 0.9216 (mmm) cc_final: 0.8785 (mmm) REVERT: A 283 MET cc_start: 0.9342 (mmm) cc_final: 0.9113 (mmm) REVERT: A 305 MET cc_start: 0.9266 (mmm) cc_final: 0.8957 (tpp) REVERT: A 355 MET cc_start: 0.9011 (mmm) cc_final: 0.8751 (mmp) REVERT: D 227 MET cc_start: 0.9243 (mmt) cc_final: 0.8559 (tpp) REVERT: D 283 MET cc_start: 0.9094 (mmm) cc_final: 0.8837 (mmm) REVERT: D 305 MET cc_start: 0.9217 (tpp) cc_final: 0.8697 (mmm) REVERT: D 313 MET cc_start: 0.9492 (mmm) cc_final: 0.9104 (tpp) REVERT: G 5 ASP cc_start: 0.8784 (m-30) cc_final: 0.8279 (t0) REVERT: B 176 MET cc_start: 0.8188 (mtp) cc_final: 0.7804 (mtt) REVERT: B 227 MET cc_start: 0.8785 (mmm) cc_final: 0.8059 (mpp) outliers start: 8 outliers final: 3 residues processed: 115 average time/residue: 0.2680 time to fit residues: 47.6963 Evaluate side-chains 112 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain D residue 356 TRP 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 93 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 188 optimal weight: 0.7980 chunk 19 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.2882 r_free = 0.2882 target = 0.033925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.028140 restraints weight = 102278.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.029341 restraints weight = 49261.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.030171 restraints weight = 30058.843| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3113 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= 0.148 Angle : 0.554 9.629 20960 Z= 0.262 Chirality : 0.043 0.139 2335 Planarity : 0.004 0.057 2670 Dihedral : 6.915 77.529 2145 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.12 % Allowed : 7.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1885 helix: 1.32 (0.19), residues: 805 sheet: 0.29 (0.30), residues: 280 loop : 0.87 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 356 HIS 0.003 0.001 HIS E 275 PHE 0.009 0.001 PHE D 255 TYR 0.016 0.001 TYR D 306 ARG 0.002 0.000 ARG E 335 *********************** 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 111 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 1.833 Fit side-chains REVERT: H 5 ASP cc_start: 0.9287 (m-30) cc_final: 0.9006 (t70) REVERT: C 313 MET cc_start: 0.9401 (mmm) cc_final: 0.8813 (tpt) REVERT: C 325 MET cc_start: 0.8268 (ttp) cc_final: 0.7974 (ttm) REVERT: E 123 MET cc_start: 0.9187 (mmt) cc_final: 0.8897 (mmt) REVERT: E 132 MET cc_start: 0.8441 (tmm) cc_final: 0.8177 (tmm) REVERT: E 227 MET cc_start: 0.9117 (mmm) cc_final: 0.8859 (tpt) REVERT: E 305 MET cc_start: 0.9450 (mmm) cc_final: 0.8905 (mmt) REVERT: E 358 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8089 (t) REVERT: A 44 MET cc_start: 0.9160 (mmm) cc_final: 0.8874 (mmm) REVERT: A 176 MET cc_start: 0.8432 (mtt) cc_final: 0.8202 (mtt) REVERT: A 305 MET cc_start: 0.9194 (mmm) cc_final: 0.8886 (tpp) REVERT: A 355 MET cc_start: 0.8978 (mmm) cc_final: 0.8726 (mmp) REVERT: D 227 MET cc_start: 0.9234 (mmt) cc_final: 0.8614 (tpp) REVERT: D 305 MET cc_start: 0.9101 (tpp) cc_final: 0.8596 (mmm) REVERT: D 313 MET cc_start: 0.9417 (mmm) cc_final: 0.9070 (tpp) REVERT: D 325 MET cc_start: 0.8918 (ttm) cc_final: 0.8717 (ttm) REVERT: G 5 ASP cc_start: 0.8866 (m-30) cc_final: 0.8380 (t0) REVERT: B 82 MET cc_start: 0.9370 (tpp) cc_final: 0.8998 (mmm) REVERT: B 227 MET cc_start: 0.8748 (mmm) cc_final: 0.7975 (mpp) REVERT: B 299 MET cc_start: 0.9025 (mmm) cc_final: 0.8325 (mmm) outliers start: 2 outliers final: 1 residues processed: 110 average time/residue: 0.2709 time to fit residues: 46.7581 Evaluate side-chains 111 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 162 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 188 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.033768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.028059 restraints weight = 102546.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.029234 restraints weight = 49339.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.030049 restraints weight = 30196.554| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15460 Z= 0.164 Angle : 0.551 10.367 20960 Z= 0.258 Chirality : 0.043 0.141 2335 Planarity : 0.004 0.056 2670 Dihedral : 6.775 77.547 2145 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.25 % Allowed : 8.02 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.20), residues: 1885 helix: 1.40 (0.19), residues: 805 sheet: 0.34 (0.30), residues: 280 loop : 0.90 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 356 HIS 0.003 0.001 HIS A 275 PHE 0.008 0.001 PHE D 255 TYR 0.011 0.001 TYR D 306 ARG 0.002 0.000 ARG A 335 *********************** 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: 4 poor density : 109 time to evaluate : 1.792 Fit side-chains REVERT: H 5 ASP cc_start: 0.9273 (m-30) cc_final: 0.9018 (t70) REVERT: C 325 MET cc_start: 0.8249 (ttp) cc_final: 0.8040 (ttm) REVERT: E 123 MET cc_start: 0.9225 (mmt) cc_final: 0.8840 (mmp) REVERT: E 132 MET cc_start: 0.8449 (tmm) cc_final: 0.8158 (tmm) REVERT: E 227 MET cc_start: 0.9124 (mmm) cc_final: 0.8856 (tpt) REVERT: E 305 MET cc_start: 0.9452 (mmm) cc_final: 0.8878 (mmt) REVERT: E 358 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8122 (t) REVERT: A 44 MET cc_start: 0.9149 (mmm) cc_final: 0.8849 (mmm) REVERT: A 47 MET cc_start: 0.6977 (mmm) cc_final: 0.6766 (mmm) REVERT: A 227 MET cc_start: 0.9196 (mmm) cc_final: 0.8765 (mmm) REVERT: A 283 MET cc_start: 0.9430 (mmm) cc_final: 0.9156 (mmm) REVERT: A 299 MET cc_start: 0.8780 (mmm) cc_final: 0.8504 (mtp) REVERT: A 305 MET cc_start: 0.9219 (mmm) cc_final: 0.8890 (tpp) REVERT: A 355 MET cc_start: 0.8958 (mmm) cc_final: 0.8652 (mmm) REVERT: D 227 MET cc_start: 0.9229 (mmt) cc_final: 0.8621 (tpp) REVERT: D 305 MET cc_start: 0.9163 (tpp) cc_final: 0.8649 (mmm) REVERT: D 313 MET cc_start: 0.9484 (mmm) cc_final: 0.9110 (tpp) REVERT: D 325 MET cc_start: 0.8919 (ttm) cc_final: 0.8688 (ttm) REVERT: G 5 ASP cc_start: 0.8827 (m-30) cc_final: 0.8345 (t0) REVERT: B 227 MET cc_start: 0.8774 (mmm) cc_final: 0.7995 (mpp) REVERT: B 299 MET cc_start: 0.9009 (mmm) cc_final: 0.8425 (mmm) outliers start: 4 outliers final: 2 residues processed: 112 average time/residue: 0.2575 time to fit residues: 44.7586 Evaluate side-chains 112 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 1.661 ------------------------------------------------------------------------------- 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 177 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 170 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 71 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 147 optimal weight: 0.5980 chunk 75 optimal weight: 0.2980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.2885 r_free = 0.2885 target = 0.033937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.028188 restraints weight = 102338.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.029380 restraints weight = 49316.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.030204 restraints weight = 30114.612| |-----------------------------------------------------------------------------| r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3269 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= 0.163 Angle : 0.554 9.182 20960 Z= 0.258 Chirality : 0.042 0.140 2335 Planarity : 0.004 0.056 2670 Dihedral : 6.648 77.491 2145 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.19 % Allowed : 8.09 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.20), residues: 1885 helix: 1.49 (0.19), residues: 805 sheet: 0.36 (0.30), residues: 280 loop : 0.96 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 356 HIS 0.003 0.001 HIS A 275 PHE 0.009 0.001 PHE D 255 TYR 0.011 0.001 TYR D 306 ARG 0.003 0.000 ARG C 335 *********************** 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: 3 poor density : 110 time to evaluate : 2.012 Fit side-chains REVERT: H 5 ASP cc_start: 0.9283 (m-30) cc_final: 0.9048 (t70) REVERT: C 325 MET cc_start: 0.8267 (ttp) cc_final: 0.8051 (ttm) REVERT: E 123 MET cc_start: 0.9220 (mmt) cc_final: 0.8844 (mmp) REVERT: E 132 MET cc_start: 0.8442 (tmm) cc_final: 0.8162 (tmm) REVERT: E 227 MET cc_start: 0.9125 (mmm) cc_final: 0.8851 (tpt) REVERT: E 305 MET cc_start: 0.9450 (mmm) cc_final: 0.8875 (mmt) REVERT: E 358 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8103 (t) REVERT: A 44 MET cc_start: 0.9139 (mmm) cc_final: 0.8181 (mmm) REVERT: A 132 MET cc_start: 0.8483 (tmm) cc_final: 0.8247 (tmm) REVERT: A 176 MET cc_start: 0.8417 (mtt) cc_final: 0.8185 (mtt) REVERT: A 227 MET cc_start: 0.9192 (mmm) cc_final: 0.8746 (mmm) REVERT: A 283 MET cc_start: 0.9446 (mmm) cc_final: 0.9220 (mmm) REVERT: A 305 MET cc_start: 0.9210 (mmm) cc_final: 0.8875 (tpp) REVERT: A 355 MET cc_start: 0.8952 (mmm) cc_final: 0.8659 (mmm) REVERT: D 227 MET cc_start: 0.9227 (mmt) cc_final: 0.8637 (tpp) REVERT: D 305 MET cc_start: 0.9148 (tpp) cc_final: 0.8694 (mmm) REVERT: D 313 MET cc_start: 0.9483 (mmm) cc_final: 0.9101 (tpp) REVERT: D 325 MET cc_start: 0.8923 (ttm) cc_final: 0.8689 (ttm) REVERT: G 5 ASP cc_start: 0.8862 (m-30) cc_final: 0.8385 (t70) REVERT: B 227 MET cc_start: 0.8790 (mmm) cc_final: 0.8008 (mpp) outliers start: 3 outliers final: 2 residues processed: 112 average time/residue: 0.2696 time to fit residues: 47.0242 Evaluate side-chains 111 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 1.818 ------------------------------------------------------------------------------- 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 89 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 183 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 188 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.2899 r_free = 0.2899 target = 0.034272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.028515 restraints weight = 102450.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.029701 restraints weight = 49138.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.030533 restraints weight = 29969.871| |-----------------------------------------------------------------------------| r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15460 Z= 0.144 Angle : 0.549 8.848 20960 Z= 0.254 Chirality : 0.042 0.140 2335 Planarity : 0.004 0.057 2670 Dihedral : 6.510 77.331 2145 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.19 % Allowed : 7.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1885 helix: 1.18 (0.18), residues: 855 sheet: 0.44 (0.30), residues: 280 loop : 0.98 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 356 HIS 0.003 0.000 HIS A 275 PHE 0.009 0.001 PHE D 255 TYR 0.013 0.001 TYR D 306 ARG 0.005 0.000 ARG C 335 ********************** 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 112 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 1.977 Fit side-chains revert: symmetry clash REVERT: H 5 ASP cc_start: 0.9244 (m-30) cc_final: 0.9017 (t70) REVERT: E 123 MET cc_start: 0.9213 (mmt) cc_final: 0.8844 (mmp) REVERT: E 132 MET cc_start: 0.8467 (tmm) cc_final: 0.8196 (tmm) REVERT: E 227 MET cc_start: 0.9122 (mmm) cc_final: 0.8844 (tpt) REVERT: E 305 MET cc_start: 0.9462 (mmm) cc_final: 0.8892 (mmt) REVERT: E 358 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8192 (t) REVERT: A 44 MET cc_start: 0.9113 (mmm) cc_final: 0.8829 (mmm) REVERT: A 132 MET cc_start: 0.8549 (tmm) cc_final: 0.8314 (tmm) REVERT: A 227 MET cc_start: 0.9222 (mmm) cc_final: 0.8779 (mmm) REVERT: A 305 MET cc_start: 0.9211 (mmm) cc_final: 0.8875 (tpp) REVERT: A 355 MET cc_start: 0.8944 (mmm) cc_final: 0.8668 (mmm) REVERT: D 227 MET cc_start: 0.9218 (mmt) cc_final: 0.8642 (tpp) REVERT: D 305 MET cc_start: 0.9128 (tpp) cc_final: 0.8674 (mmm) REVERT: D 313 MET cc_start: 0.9483 (mmm) cc_final: 0.9107 (tpp) REVERT: G 5 ASP cc_start: 0.8828 (m-30) cc_final: 0.8348 (t70) REVERT: B 82 MET cc_start: 0.9370 (tpp) cc_final: 0.8974 (mmm) REVERT: B 227 MET cc_start: 0.8786 (mmm) cc_final: 0.7997 (mpp) REVERT: B 299 MET cc_start: 0.8951 (mmm) cc_final: 0.8507 (mmm) outliers start: 3 outliers final: 2 residues processed: 111 average time/residue: 0.2596 time to fit residues: 44.9176 Evaluate side-chains 112 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 1.940 ------------------------------------------------------------------------------- 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.0453 > 50: distance: 63 - 67: 27.696 distance: 67 - 68: 36.953 distance: 68 - 69: 20.424 distance: 68 - 71: 29.884 distance: 69 - 70: 22.024 distance: 69 - 75: 34.861 distance: 71 - 72: 4.020 distance: 72 - 73: 5.933 distance: 72 - 74: 53.410 distance: 75 - 76: 56.332 distance: 76 - 77: 41.003 distance: 76 - 79: 13.736 distance: 77 - 86: 40.991 distance: 79 - 80: 41.796 distance: 80 - 81: 45.811 distance: 81 - 82: 6.334 distance: 82 - 83: 42.033 distance: 83 - 84: 26.122 distance: 83 - 85: 28.744 distance: 86 - 87: 7.738 distance: 87 - 90: 39.648 distance: 90 - 91: 18.101 distance: 93 - 94: 39.051 distance: 94 - 95: 64.519 distance: 94 - 97: 42.484 distance: 95 - 96: 30.660 distance: 95 - 98: 11.649 distance: 96 - 114: 30.017 distance: 98 - 99: 55.185 distance: 98 - 104: 45.468 distance: 99 - 100: 47.633 distance: 99 - 102: 42.258 distance: 100 - 101: 26.556 distance: 100 - 105: 40.001 distance: 101 - 123: 20.379 distance: 102 - 103: 66.668 distance: 103 - 104: 41.778 distance: 105 - 106: 8.393 distance: 106 - 107: 19.238 distance: 106 - 109: 17.242 distance: 107 - 114: 22.990 distance: 109 - 110: 30.385 distance: 110 - 111: 10.268 distance: 111 - 112: 30.213 distance: 111 - 113: 16.353 distance: 114 - 115: 26.771 distance: 115 - 116: 50.929 distance: 115 - 118: 28.047 distance: 116 - 117: 35.207 distance: 116 - 123: 49.110 distance: 118 - 119: 17.174 distance: 119 - 120: 17.079 distance: 120 - 121: 7.117 distance: 120 - 122: 3.767 distance: 123 - 124: 25.681 distance: 124 - 125: 41.650 distance: 124 - 127: 35.675 distance: 125 - 126: 52.220 distance: 125 - 133: 30.589 distance: 127 - 128: 8.017 distance: 128 - 129: 30.462 distance: 128 - 130: 8.830 distance: 129 - 131: 14.006 distance: 131 - 132: 18.897 distance: 133 - 134: 52.413 distance: 133 - 139: 9.421 distance: 134 - 135: 10.216 distance: 134 - 137: 11.456 distance: 135 - 136: 30.795 distance: 135 - 140: 39.891 distance: 137 - 138: 37.599 distance: 138 - 139: 31.880 distance: 141 - 142: 13.093 distance: 141 - 144: 23.784 distance: 142 - 143: 9.222 distance: 142 - 147: 25.751 distance: 144 - 146: 23.242