Starting phenix.real_space_refine on Fri Jun 13 18:57:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvx_17979/06_2025/8pvx_17979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvx_17979/06_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_17979/06_2025/8pvx_17979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvx_17979/06_2025/8pvx_17979.map" model { file = "/net/cci-nas-00/data/ceres_data/8pvx_17979/06_2025/8pvx_17979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvx_17979/06_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-5710/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: 9.81, per 1000 atoms: 0.65 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: 4.75 Conformation dependent library (CDL) restraints added in 2.1 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: 1.97 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: 5.53 Time building geometry restraints manager: 5.18 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.240 Find NCS groups from input model: 0.640 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15460 Z= 0.169 Angle : 0.795 10.962 20960 Z= 0.438 Chirality : 0.050 0.246 2335 Planarity : 0.009 0.116 2670 Dihedral : 13.294 120.875 5755 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.15795 ( 751) hydrogen bonds : angle 7.13173 ( 1971) covalent geometry : bond 0.00333 (15460) covalent geometry : angle 0.79495 (20960) *********************** 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 : 1.757 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: 0.2666 time to fit residues: 51.5245 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 : 1.722 ------------------------------------------------------------------------------- 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 = 0.035153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.029501 restraints weight = 101902.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.030725 restraints weight = 47963.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.031573 restraints weight = 28891.021| |-----------------------------------------------------------------------------| 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= 0.141 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 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 751) hydrogen bonds : angle 5.28778 ( 1971) covalent geometry : bond 0.00308 (15460) covalent geometry : angle 0.62813 (20960) *********************** 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 : 1.599 Fit side-chains REVERT: C 227 MET cc_start: 0.8923 (mmm) cc_final: 0.8625 (mmm) REVERT: C 269 MET cc_start: 0.9113 (mtm) cc_final: 0.8722 (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: 0.8217 (tmm) cc_final: 0.8009 (tmm) REVERT: E 283 MET cc_start: 0.9312 (mmp) cc_final: 0.9073 (mmm) REVERT: E 305 MET cc_start: 0.9409 (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: 0.9131 (mmm) cc_final: 0.8859 (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: 0.2601 time to fit residues: 46.6237 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 : 1.648 ------------------------------------------------------------------------------- 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: 6.9990 chunk 185 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 140 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 = 0.2837 r_free = 0.2837 target = 0.032805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.027105 restraints weight = 103850.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.028263 restraints weight = 50226.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.029073 restraints weight = 30912.895| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 15460 Z= 0.286 Angle : 0.676 7.013 20960 Z= 0.334 Chirality : 0.047 0.165 2335 Planarity : 0.005 0.064 2670 Dihedral : 8.013 84.871 2145 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.25 % Allowed : 3.77 % Favored : 95.99 % 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: 0.89 (0.20), residues: 1885 helix: 0.74 (0.18), residues: 835 sheet: 0.72 (0.29), residues: 280 loop : 0.59 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 356 HIS 0.009 0.002 HIS D 88 PHE 0.017 0.002 PHE B 262 TYR 0.012 0.002 TYR A 306 ARG 0.005 0.001 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 751) hydrogen bonds : angle 5.31507 ( 1971) covalent geometry : bond 0.00638 (15460) covalent geometry : angle 0.67592 (20960) *********************** 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 117 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 1.797 Fit side-chains REVERT: C 176 MET cc_start: 0.8921 (mtt) cc_final: 0.8699 (mtt) REVERT: C 269 MET cc_start: 0.9146 (mtm) cc_final: 0.8893 (mtp) REVERT: C 313 MET cc_start: 0.9342 (mmm) cc_final: 0.8806 (tpt) REVERT: E 123 MET cc_start: 0.9219 (mmt) cc_final: 0.8874 (mmp) REVERT: E 283 MET cc_start: 0.9298 (mmp) cc_final: 0.9040 (mmm) REVERT: E 305 MET cc_start: 0.9362 (mmm) cc_final: 0.8818 (mmt) REVERT: A 44 MET cc_start: 0.8972 (mmm) cc_final: 0.8691 (mmm) REVERT: A 305 MET cc_start: 0.9261 (mmm) cc_final: 0.8977 (tpp) REVERT: A 355 MET cc_start: 0.8957 (mmm) cc_final: 0.8605 (mmm) REVERT: D 227 MET cc_start: 0.9257 (mmt) cc_final: 0.8616 (tpp) REVERT: D 313 MET cc_start: 0.9477 (mmm) cc_final: 0.8680 (tpt) REVERT: G 5 ASP cc_start: 0.8668 (m-30) cc_final: 0.8357 (t0) outliers start: 4 outliers final: 1 residues processed: 114 average time/residue: 0.2692 time to fit residues: 47.2131 Evaluate side-chains 109 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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: 4.9990 chunk 163 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.033714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.027961 restraints weight = 102437.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.029149 restraints weight = 49159.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.029970 restraints weight = 30078.824| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15460 Z= 0.138 Angle : 0.572 8.334 20960 Z= 0.275 Chirality : 0.043 0.140 2335 Planarity : 0.004 0.061 2670 Dihedral : 7.342 78.657 2145 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.12 % Allowed : 4.94 % Favored : 94.94 % 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: 1.11 (0.20), residues: 1885 helix: 0.92 (0.18), residues: 835 sheet: 0.67 (0.30), residues: 280 loop : 0.79 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 356 HIS 0.003 0.001 HIS A 275 PHE 0.009 0.001 PHE D 255 TYR 0.016 0.001 TYR D 306 ARG 0.003 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.03300 ( 751) hydrogen bonds : angle 4.89287 ( 1971) covalent geometry : bond 0.00309 (15460) covalent geometry : angle 0.57242 (20960) *********************** 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: 2 poor density : 112 time to evaluate : 2.845 Fit side-chains REVERT: C 305 MET cc_start: 0.9129 (mmm) cc_final: 0.8828 (tpp) REVERT: C 313 MET cc_start: 0.9334 (mmm) cc_final: 0.8830 (tpt) REVERT: C 325 MET cc_start: 0.8119 (ttp) cc_final: 0.7632 (ttm) REVERT: J 10 PHE cc_start: 0.7807 (m-80) cc_final: 0.7548 (m-80) REVERT: E 123 MET cc_start: 0.9242 (mmt) cc_final: 0.8801 (mmp) REVERT: E 305 MET cc_start: 0.9454 (mmm) cc_final: 0.8909 (mmt) REVERT: E 358 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.7912 (t) REVERT: A 44 MET cc_start: 0.9041 (mmm) cc_final: 0.8734 (mmm) REVERT: A 176 MET cc_start: 0.8361 (mtt) cc_final: 0.8142 (mtt) REVERT: A 305 MET cc_start: 0.9184 (mmm) cc_final: 0.8933 (tpp) REVERT: A 355 MET cc_start: 0.8970 (mmm) cc_final: 0.8674 (mmm) REVERT: D 227 MET cc_start: 0.9240 (mmt) cc_final: 0.8644 (tpp) REVERT: D 269 MET cc_start: 0.8968 (mtp) cc_final: 0.8762 (mtp) REVERT: D 283 MET cc_start: 0.9125 (mmm) cc_final: 0.8883 (mmm) REVERT: D 305 MET cc_start: 0.9190 (tpp) cc_final: 0.8664 (mmm) REVERT: D 313 MET cc_start: 0.9441 (mmm) cc_final: 0.9055 (tpp) REVERT: G 5 ASP cc_start: 0.8692 (m-30) cc_final: 0.8354 (t0) outliers start: 2 outliers final: 1 residues processed: 114 average time/residue: 0.2946 time to fit residues: 52.8317 Evaluate side-chains 113 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 146 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 36 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 = 0.2861 r_free = 0.2861 target = 0.033413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.027659 restraints weight = 103727.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.028823 restraints weight = 49993.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.029653 restraints weight = 30709.427| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15460 Z= 0.161 Angle : 0.569 7.154 20960 Z= 0.272 Chirality : 0.043 0.138 2335 Planarity : 0.004 0.060 2670 Dihedral : 7.142 77.476 2145 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.31 % Allowed : 5.99 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.20), residues: 1885 helix: 1.26 (0.19), residues: 805 sheet: 0.53 (0.29), residues: 280 loop : 0.88 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 356 HIS 0.004 0.001 HIS D 88 PHE 0.009 0.001 PHE B 262 TYR 0.011 0.001 TYR A 306 ARG 0.003 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 751) hydrogen bonds : angle 4.80628 ( 1971) covalent geometry : bond 0.00363 (15460) covalent geometry : angle 0.56889 (20960) *********************** 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 117 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 112 time to evaluate : 2.517 Fit side-chains revert: symmetry clash REVERT: H 5 ASP cc_start: 0.9324 (m-30) cc_final: 0.8971 (t70) REVERT: C 305 MET cc_start: 0.9151 (mmm) cc_final: 0.8926 (tpp) REVERT: C 313 MET cc_start: 0.9389 (mmm) cc_final: 0.8824 (tpt) REVERT: C 325 MET cc_start: 0.8214 (ttp) cc_final: 0.7984 (ttm) REVERT: E 123 MET cc_start: 0.9243 (mmt) cc_final: 0.8900 (mmp) REVERT: E 132 MET cc_start: 0.8360 (tmm) cc_final: 0.8096 (tmm) REVERT: E 305 MET cc_start: 0.9453 (mmm) cc_final: 0.8895 (mmt) REVERT: E 358 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8029 (t) REVERT: A 44 MET cc_start: 0.9115 (mmm) cc_final: 0.8801 (mmm) REVERT: A 227 MET cc_start: 0.9263 (mmm) cc_final: 0.8853 (mmm) REVERT: A 305 MET cc_start: 0.9261 (mmm) cc_final: 0.8984 (tpp) REVERT: D 313 MET cc_start: 0.9449 (mmm) cc_final: 0.9051 (tpp) REVERT: G 5 ASP cc_start: 0.8758 (m-30) cc_final: 0.8393 (t0) REVERT: B 227 MET cc_start: 0.8736 (mmm) cc_final: 0.8031 (mpp) outliers start: 5 outliers final: 1 residues processed: 114 average time/residue: 0.2672 time to fit residues: 48.0537 Evaluate side-chains 113 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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: 0.1980 chunk 62 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 157 optimal weight: 0.0870 chunk 85 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 overall best weight: 2.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.033294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.027569 restraints weight = 103314.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.028719 restraints weight = 49854.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.029535 restraints weight = 30699.910| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15460 Z= 0.178 Angle : 0.579 9.617 20960 Z= 0.276 Chirality : 0.044 0.137 2335 Planarity : 0.004 0.057 2670 Dihedral : 7.077 77.584 2145 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.31 % Allowed : 6.67 % Favored : 93.02 % 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: 1.46 (0.20), residues: 1885 helix: 1.49 (0.19), residues: 775 sheet: 0.39 (0.29), residues: 280 loop : 0.88 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 79 HIS 0.004 0.001 HIS D 88 PHE 0.010 0.001 PHE D 255 TYR 0.010 0.001 TYR A 306 ARG 0.005 0.000 ARG E 256 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 751) hydrogen bonds : angle 4.78864 ( 1971) covalent geometry : bond 0.00399 (15460) covalent geometry : angle 0.57905 (20960) *********************** 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 115 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 1.737 Fit side-chains REVERT: H 5 ASP cc_start: 0.9312 (m-30) cc_final: 0.8981 (t70) REVERT: C 325 MET cc_start: 0.8269 (ttp) cc_final: 0.8015 (ttm) REVERT: E 123 MET cc_start: 0.9249 (mmt) cc_final: 0.8914 (mmp) REVERT: E 132 MET cc_start: 0.8411 (tmm) cc_final: 0.7969 (tmm) REVERT: E 305 MET cc_start: 0.9438 (mmm) cc_final: 0.8885 (mmt) REVERT: E 358 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.8058 (t) REVERT: F 9 LYS cc_start: 0.8774 (pttt) cc_final: 0.8306 (pptt) REVERT: A 44 MET cc_start: 0.9124 (mmm) cc_final: 0.8807 (mmm) REVERT: A 283 MET cc_start: 0.9373 (mmm) cc_final: 0.9163 (mmm) REVERT: A 305 MET cc_start: 0.9261 (mmm) cc_final: 0.8965 (tpp) REVERT: A 355 MET cc_start: 0.8924 (mmm) cc_final: 0.8695 (mmp) REVERT: D 283 MET cc_start: 0.9092 (mmm) cc_final: 0.8830 (mmm) REVERT: D 305 MET cc_start: 0.9179 (tpp) cc_final: 0.8652 (mmm) REVERT: D 313 MET cc_start: 0.9471 (mmm) cc_final: 0.9089 (tpp) REVERT: G 5 ASP cc_start: 0.8816 (m-30) cc_final: 0.8409 (t0) REVERT: B 227 MET cc_start: 0.8761 (mmm) cc_final: 0.8020 (mpp) outliers start: 5 outliers final: 2 residues processed: 113 average time/residue: 0.3128 time to fit residues: 56.2097 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 : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain A residue 269 MET 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: 0.7980 chunk 109 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.033860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.028084 restraints weight = 102983.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.029274 restraints weight = 49623.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.030106 restraints weight = 30422.451| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15460 Z= 0.116 Angle : 0.547 7.163 20960 Z= 0.258 Chirality : 0.043 0.138 2335 Planarity : 0.004 0.057 2670 Dihedral : 6.838 77.308 2145 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.25 % Allowed : 7.41 % Favored : 92.35 % 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: 1.59 (0.20), residues: 1885 helix: 1.60 (0.19), residues: 775 sheet: 0.38 (0.30), residues: 280 loop : 0.97 (0.24), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 356 HIS 0.003 0.001 HIS A 275 PHE 0.008 0.001 PHE D 255 TYR 0.012 0.001 TYR D 306 ARG 0.002 0.000 ARG E 335 Details of bonding type rmsd hydrogen bonds : bond 0.02930 ( 751) hydrogen bonds : angle 4.62317 ( 1971) covalent geometry : bond 0.00262 (15460) covalent geometry : angle 0.54659 (20960) *********************** 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 113 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 2.595 Fit side-chains REVERT: H 5 ASP cc_start: 0.9304 (m-30) cc_final: 0.8998 (t70) REVERT: C 313 MET cc_start: 0.9432 (mmm) cc_final: 0.8862 (tpt) REVERT: C 325 MET cc_start: 0.8249 (ttp) cc_final: 0.8000 (ttm) REVERT: E 123 MET cc_start: 0.9241 (mmt) cc_final: 0.8839 (mmp) REVERT: E 132 MET cc_start: 0.8452 (tmm) cc_final: 0.8052 (tmm) REVERT: E 305 MET cc_start: 0.9459 (mmm) cc_final: 0.8913 (mmt) REVERT: E 358 THR cc_start: 0.8405 (OUTLIER) cc_final: 0.8136 (t) REVERT: A 44 MET cc_start: 0.9120 (mmm) cc_final: 0.8846 (mmm) REVERT: A 227 MET cc_start: 0.9227 (mmm) cc_final: 0.8807 (mmm) REVERT: A 305 MET cc_start: 0.9212 (mmm) cc_final: 0.8902 (tpp) REVERT: D 227 MET cc_start: 0.9081 (tpp) cc_final: 0.8699 (tpp) REVERT: D 269 MET cc_start: 0.8964 (mtp) cc_final: 0.8740 (mtp) REVERT: D 305 MET cc_start: 0.9098 (tpp) cc_final: 0.8602 (mmm) REVERT: D 313 MET cc_start: 0.9446 (mmm) cc_final: 0.9076 (tpp) REVERT: G 5 ASP cc_start: 0.8828 (m-30) cc_final: 0.8398 (t0) REVERT: B 227 MET cc_start: 0.8741 (mmm) cc_final: 0.7956 (mpp) REVERT: B 313 MET cc_start: 0.9459 (tpp) cc_final: 0.9242 (mmt) outliers start: 4 outliers final: 1 residues processed: 112 average time/residue: 0.3707 time to fit residues: 67.4621 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 : 1.762 ------------------------------------------------------------------------------- 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: 0.8980 chunk 104 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 188 optimal weight: 0.8980 chunk 100 optimal weight: 0.0470 chunk 173 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- 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 = 0.2901 r_free = 0.2901 target = 0.034290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.028523 restraints weight = 101876.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.029724 restraints weight = 48971.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.030557 restraints weight = 29868.847| |-----------------------------------------------------------------------------| r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3176 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= 0.096 Angle : 0.544 7.817 20960 Z= 0.253 Chirality : 0.042 0.139 2335 Planarity : 0.004 0.057 2670 Dihedral : 6.637 77.706 2145 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.25 % Allowed : 7.53 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.55 (0.20), residues: 1885 helix: 1.46 (0.19), residues: 815 sheet: 0.44 (0.30), residues: 280 loop : 1.02 (0.24), residues: 790 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 0.012 0.001 TYR D 306 ARG 0.003 0.000 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.02748 ( 751) hydrogen bonds : angle 4.51517 ( 1971) covalent geometry : bond 0.00219 (15460) covalent geometry : angle 0.54436 (20960) *********************** 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 114 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 1.637 Fit side-chains REVERT: H 5 ASP cc_start: 0.9288 (m-30) cc_final: 0.9042 (t70) REVERT: C 313 MET cc_start: 0.9422 (mmm) cc_final: 0.8855 (tpt) REVERT: C 325 MET cc_start: 0.8150 (ttp) cc_final: 0.7946 (ttm) REVERT: E 123 MET cc_start: 0.9232 (mmt) cc_final: 0.8838 (mmp) REVERT: E 132 MET cc_start: 0.8500 (tmm) cc_final: 0.8071 (tmm) REVERT: E 305 MET cc_start: 0.9467 (mmm) cc_final: 0.8898 (mmt) REVERT: E 358 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8163 (t) REVERT: A 44 MET cc_start: 0.9133 (mmm) cc_final: 0.8910 (mmm) REVERT: A 176 MET cc_start: 0.8418 (mtt) cc_final: 0.8185 (mtt) REVERT: A 299 MET cc_start: 0.8789 (mmm) cc_final: 0.8557 (mtp) REVERT: A 305 MET cc_start: 0.9215 (mmm) cc_final: 0.8906 (tpp) REVERT: D 227 MET cc_start: 0.9028 (tpp) cc_final: 0.8654 (tpp) REVERT: D 269 MET cc_start: 0.8914 (mtp) cc_final: 0.8704 (mtp) REVERT: D 305 MET cc_start: 0.9095 (tpp) cc_final: 0.8630 (mmm) REVERT: D 313 MET cc_start: 0.9440 (mmm) cc_final: 0.9066 (tpp) REVERT: G 5 ASP cc_start: 0.8745 (m-30) cc_final: 0.8257 (t0) REVERT: B 82 MET cc_start: 0.9383 (tpp) cc_final: 0.9000 (mmm) REVERT: B 227 MET cc_start: 0.8776 (mmm) cc_final: 0.7990 (mpp) REVERT: B 313 MET cc_start: 0.9453 (tpp) cc_final: 0.9248 (mmt) outliers start: 4 outliers final: 1 residues processed: 113 average time/residue: 0.2530 time to fit residues: 44.2681 Evaluate side-chains 110 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain E residue 358 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 170 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 147 optimal weight: 0.0770 chunk 75 optimal weight: 0.9980 overall best weight: 2.8144 ------------------------------------------------------------------------------- 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 = 0.2858 r_free = 0.2858 target = 0.033249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.027517 restraints weight = 103530.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.028671 restraints weight = 50159.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.029488 restraints weight = 30844.916| |-----------------------------------------------------------------------------| r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 15460 Z= 0.179 Angle : 0.591 10.176 20960 Z= 0.277 Chirality : 0.044 0.140 2335 Planarity : 0.004 0.054 2670 Dihedral : 6.762 77.770 2145 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.25 % Allowed : 7.65 % Favored : 92.10 % 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: 1.54 (0.20), residues: 1885 helix: 1.52 (0.19), residues: 805 sheet: 0.41 (0.30), residues: 280 loop : 0.94 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.004 0.001 HIS D 88 PHE 0.009 0.001 PHE A 262 TYR 0.008 0.001 TYR E 279 ARG 0.004 0.000 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 751) hydrogen bonds : angle 4.68792 ( 1971) covalent geometry : bond 0.00403 (15460) covalent geometry : angle 0.59126 (20960) *********************** 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: 4 poor density : 109 time to evaluate : 2.136 Fit side-chains REVERT: H 5 ASP cc_start: 0.9308 (m-30) cc_final: 0.9061 (t70) REVERT: C 123 MET cc_start: 0.9225 (tpp) cc_final: 0.8897 (tpp) REVERT: C 325 MET cc_start: 0.8340 (ttp) cc_final: 0.8062 (ttm) REVERT: E 123 MET cc_start: 0.9209 (mmt) cc_final: 0.8786 (mmp) REVERT: E 305 MET cc_start: 0.9431 (mmm) cc_final: 0.8842 (mmt) REVERT: E 358 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8111 (t) REVERT: A 44 MET cc_start: 0.9145 (mmm) cc_final: 0.8872 (mmm) REVERT: A 176 MET cc_start: 0.8402 (mtt) cc_final: 0.8179 (mtt) REVERT: A 227 MET cc_start: 0.9184 (mmm) cc_final: 0.8768 (mmm) REVERT: A 283 MET cc_start: 0.9381 (mmm) cc_final: 0.9153 (mmm) REVERT: A 305 MET cc_start: 0.9268 (mmm) cc_final: 0.8955 (tpp) REVERT: D 227 MET cc_start: 0.9065 (tpp) cc_final: 0.8572 (tpp) REVERT: D 269 MET cc_start: 0.8974 (mtp) cc_final: 0.8742 (mtp) REVERT: D 305 MET cc_start: 0.9152 (tpp) cc_final: 0.8634 (mmm) REVERT: D 313 MET cc_start: 0.9501 (mmm) cc_final: 0.9101 (tpp) REVERT: G 5 ASP cc_start: 0.8911 (m-30) cc_final: 0.8432 (t70) REVERT: B 227 MET cc_start: 0.8787 (mmm) cc_final: 0.7989 (mpp) REVERT: B 313 MET cc_start: 0.9464 (tpp) cc_final: 0.9249 (mmt) outliers start: 4 outliers final: 3 residues processed: 111 average time/residue: 0.2825 time to fit residues: 48.9140 Evaluate side-chains 111 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain G residue 9 LYS 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: 0.1980 chunk 116 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 126 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 188 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.2906 r_free = 0.2906 target = 0.034444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.028674 restraints weight = 102280.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.029840 restraints weight = 48832.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.030679 restraints weight = 29916.861| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15460 Z= 0.090 Angle : 0.556 9.462 20960 Z= 0.257 Chirality : 0.042 0.138 2335 Planarity : 0.004 0.056 2670 Dihedral : 6.538 77.750 2145 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.25 % Allowed : 7.84 % Favored : 91.91 % 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: 1.61 (0.20), residues: 1885 helix: 1.50 (0.19), residues: 815 sheet: 0.45 (0.30), residues: 280 loop : 1.07 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 356 HIS 0.003 0.000 HIS A 275 PHE 0.010 0.001 PHE D 255 TYR 0.015 0.001 TYR D 306 ARG 0.002 0.000 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.02651 ( 751) hydrogen bonds : angle 4.50379 ( 1971) covalent geometry : bond 0.00205 (15460) covalent geometry : angle 0.55589 (20960) ********************** 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 113 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 109 time to evaluate : 1.669 Fit side-chains REVERT: H 5 ASP cc_start: 0.9243 (m-30) cc_final: 0.9013 (t70) REVERT: C 123 MET cc_start: 0.9152 (tpp) cc_final: 0.8778 (tpp) REVERT: C 313 MET cc_start: 0.9417 (mmm) cc_final: 0.8846 (tpt) REVERT: E 123 MET cc_start: 0.9202 (mmt) cc_final: 0.8833 (mmp) REVERT: E 305 MET cc_start: 0.9459 (mmm) cc_final: 0.8884 (mmt) REVERT: A 44 MET cc_start: 0.9133 (mmm) cc_final: 0.8899 (mmm) REVERT: A 227 MET cc_start: 0.9179 (mmm) cc_final: 0.8751 (mmm) REVERT: A 283 MET cc_start: 0.9441 (mmm) cc_final: 0.9158 (mmm) REVERT: A 305 MET cc_start: 0.9194 (mmm) cc_final: 0.8855 (tpp) REVERT: D 227 MET cc_start: 0.9000 (tpp) cc_final: 0.8633 (tpp) REVERT: D 269 MET cc_start: 0.8919 (mtp) cc_final: 0.8706 (mtp) REVERT: D 305 MET cc_start: 0.9085 (tpp) cc_final: 0.8682 (mmm) REVERT: D 313 MET cc_start: 0.9446 (mmm) cc_final: 0.9145 (tpp) REVERT: G 5 ASP cc_start: 0.8827 (m-30) cc_final: 0.8331 (t70) REVERT: B 82 MET cc_start: 0.9375 (tpp) cc_final: 0.8981 (mmm) REVERT: B 227 MET cc_start: 0.8771 (mmm) cc_final: 0.7984 (mpp) outliers start: 4 outliers final: 3 residues processed: 110 average time/residue: 0.2621 time to fit residues: 44.5704 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 : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain G residue 9 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 148 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 86 optimal weight: 0.0570 chunk 173 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- 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 = 0.2911 r_free = 0.2911 target = 0.034514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.028722 restraints weight = 101524.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.029931 restraints weight = 49342.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.030766 restraints weight = 30027.783| |-----------------------------------------------------------------------------| r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15460 Z= 0.090 Angle : 0.554 9.256 20960 Z= 0.255 Chirality : 0.042 0.140 2335 Planarity : 0.004 0.055 2670 Dihedral : 6.410 77.492 2145 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.12 % Allowed : 7.96 % Favored : 91.91 % 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: 1.77 (0.20), residues: 1885 helix: 1.63 (0.19), residues: 810 sheet: 0.55 (0.31), residues: 280 loop : 1.14 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 356 HIS 0.003 0.000 HIS A 275 PHE 0.009 0.001 PHE D 255 TYR 0.011 0.001 TYR D 306 ARG 0.002 0.000 ARG C 335 Details of bonding type rmsd hydrogen bonds : bond 0.02634 ( 751) hydrogen bonds : angle 4.45627 ( 1971) covalent geometry : bond 0.00207 (15460) covalent geometry : angle 0.55420 (20960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3864.43 seconds wall clock time: 72 minutes 34.42 seconds (4354.42 seconds total)