Starting phenix.real_space_refine on Fri Sep 27 07:30:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvx_17979/09_2024/8pvx_17979.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvx_17979/09_2024/8pvx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvx_17979/09_2024/8pvx_17979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvx_17979/09_2024/8pvx_17979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvx_17979/09_2024/8pvx_17979.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvx_17979/09_2024/8pvx_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-5461/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: 8.81, per 1000 atoms: 0.58 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: 3.71 Conformation dependent library (CDL) restraints added in 1.8 seconds 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3550 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 30 sheets defined 53.6% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 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: 4.81 Time building geometry restraints manager: 4.30 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.370 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15460 Z= 0.225 Angle : 0.795 10.962 20960 Z= 0.438 Chirality : 0.050 0.246 2335 Planarity : 0.009 0.116 2670 Dihedral : 13.294 120.875 5755 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 1885 helix: -0.59 (0.15), residues: 825 sheet: 0.61 (0.27), residues: 310 loop : 0.17 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.005 TRP E 356 HIS 0.004 0.001 HIS B 101 PHE 0.017 0.002 PHE B 255 TYR 0.028 0.005 TYR A 306 ARG 0.029 0.004 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.720 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: 0.2557 time to fit residues: 48.8892 Evaluate side-chains 111 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.639 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15460 Z= 0.201 Angle : 0.628 8.151 20960 Z= 0.309 Chirality : 0.045 0.187 2335 Planarity : 0.005 0.070 2670 Dihedral : 8.467 89.956 2145 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.31 % Allowed : 2.47 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 1885 helix: 0.62 (0.17), residues: 845 sheet: 1.08 (0.29), residues: 280 loop : 0.52 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 86 HIS 0.003 0.001 HIS D 88 PHE 0.019 0.001 PHE D 375 TYR 0.019 0.002 TYR A 306 ARG 0.006 0.001 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 2.009 Fit side-chains REVERT: C 227 MET cc_start: 0.9016 (mmm) cc_final: 0.8729 (mmm) REVERT: C 269 MET cc_start: 0.8979 (mtm) cc_final: 0.8692 (mtp) REVERT: C 313 MET cc_start: 0.9124 (mmm) cc_final: 0.8730 (tpt) REVERT: C 325 MET cc_start: 0.7794 (ttp) cc_final: 0.7386 (ttm) REVERT: J 7 ILE cc_start: 0.8893 (mt) cc_final: 0.8679 (mm) REVERT: E 123 MET cc_start: 0.9085 (mmt) cc_final: 0.8657 (mmp) REVERT: E 305 MET cc_start: 0.9341 (mmm) cc_final: 0.9114 (mmt) REVERT: A 283 MET cc_start: 0.9323 (mmm) cc_final: 0.9085 (mmm) REVERT: A 305 MET cc_start: 0.9067 (mmm) cc_final: 0.8816 (tpp) REVERT: A 355 MET cc_start: 0.8855 (mmm) cc_final: 0.8635 (mmp) REVERT: D 313 MET cc_start: 0.9423 (mmm) cc_final: 0.8683 (tpt) REVERT: G 5 ASP cc_start: 0.8598 (m-30) cc_final: 0.8386 (t0) REVERT: B 47 MET cc_start: 0.7109 (mmm) cc_final: 0.6880 (mmm) outliers start: 5 outliers final: 1 residues processed: 116 average time/residue: 0.2740 time to fit residues: 48.7915 Evaluate side-chains 114 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.700 ------------------------------------------------------------------------------- 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 95 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 186 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 15460 Z= 0.483 Angle : 0.702 7.133 20960 Z= 0.347 Chirality : 0.048 0.176 2335 Planarity : 0.005 0.064 2670 Dihedral : 8.117 85.844 2145 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.25 % Allowed : 3.64 % Favored : 96.11 % 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: 0.77 (0.19), residues: 1885 helix: 0.65 (0.18), residues: 845 sheet: 0.69 (0.29), residues: 280 loop : 0.52 (0.24), residues: 760 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 0.018 0.002 PHE B 262 TYR 0.011 0.002 TYR D 91 ARG 0.005 0.001 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.894 Fit side-chains REVERT: C 313 MET cc_start: 0.9258 (mmm) cc_final: 0.8723 (tpt) REVERT: E 123 MET cc_start: 0.9114 (mmt) cc_final: 0.8775 (mmp) REVERT: E 305 MET cc_start: 0.9312 (mmm) cc_final: 0.8817 (mmt) REVERT: A 305 MET cc_start: 0.9190 (mmm) cc_final: 0.8931 (tpp) REVERT: A 355 MET cc_start: 0.8853 (mmm) cc_final: 0.8564 (mmm) REVERT: D 227 MET cc_start: 0.9325 (mmt) cc_final: 0.8706 (tpp) REVERT: D 313 MET cc_start: 0.9511 (mmm) cc_final: 0.8715 (tpt) REVERT: G 5 ASP cc_start: 0.8588 (m-30) cc_final: 0.8283 (t0) outliers start: 4 outliers final: 1 residues processed: 113 average time/residue: 0.2628 time to fit residues: 45.5154 Evaluate side-chains 109 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 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 : 0.002 0.030 15460 Z= 0.163 Angle : 0.563 8.369 20960 Z= 0.271 Chirality : 0.043 0.140 2335 Planarity : 0.004 0.062 2670 Dihedral : 7.298 77.720 2145 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.19 % Allowed : 4.75 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.12 (0.20), residues: 1885 helix: 0.91 (0.18), residues: 835 sheet: 0.69 (0.30), residues: 280 loop : 0.82 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 356 HIS 0.004 0.001 HIS A 275 PHE 0.009 0.001 PHE D 255 TYR 0.019 0.001 TYR D 306 ARG 0.003 0.000 ARG A 290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 1.651 Fit side-chains REVERT: C 305 MET cc_start: 0.9045 (mmm) cc_final: 0.8762 (tpp) REVERT: C 313 MET cc_start: 0.9210 (mmm) cc_final: 0.8727 (tpt) REVERT: C 325 MET cc_start: 0.7916 (ttp) cc_final: 0.7441 (ttm) REVERT: J 10 PHE cc_start: 0.7891 (m-80) cc_final: 0.7598 (m-80) REVERT: E 132 MET cc_start: 0.8309 (tmm) cc_final: 0.7830 (tmm) REVERT: E 305 MET cc_start: 0.9392 (mmm) cc_final: 0.8902 (mmt) REVERT: E 358 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.7995 (t) REVERT: A 305 MET cc_start: 0.9105 (mmm) cc_final: 0.8861 (tpp) REVERT: A 355 MET cc_start: 0.8849 (mmm) cc_final: 0.8644 (mmm) REVERT: D 305 MET cc_start: 0.9122 (tpp) cc_final: 0.8721 (mmm) REVERT: D 313 MET cc_start: 0.9447 (mmm) cc_final: 0.9085 (tpp) REVERT: G 5 ASP cc_start: 0.8629 (m-30) cc_final: 0.8332 (t0) outliers start: 3 outliers final: 1 residues processed: 117 average time/residue: 0.2849 time to fit residues: 50.6707 Evaluate side-chains 113 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 1.798 ------------------------------------------------------------------------------- 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 152 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 136 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 15460 Z= 0.394 Angle : 0.642 7.403 20960 Z= 0.310 Chirality : 0.046 0.154 2335 Planarity : 0.004 0.059 2670 Dihedral : 7.415 79.607 2145 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.31 % Allowed : 5.68 % Favored : 94.01 % 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: 1.02 (0.20), residues: 1885 helix: 0.92 (0.18), residues: 835 sheet: 0.38 (0.29), residues: 280 loop : 0.76 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.006 0.001 HIS D 88 PHE 0.014 0.002 PHE B 262 TYR 0.011 0.001 TYR E 279 ARG 0.005 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 110 time to evaluate : 1.773 Fit side-chains REVERT: C 305 MET cc_start: 0.9098 (mmm) cc_final: 0.8843 (tpp) REVERT: C 313 MET cc_start: 0.9356 (mmm) cc_final: 0.8808 (tpt) REVERT: C 325 MET cc_start: 0.8158 (ttp) cc_final: 0.7876 (ttm) REVERT: E 123 MET cc_start: 0.9151 (mmp) cc_final: 0.8789 (mmp) REVERT: E 305 MET cc_start: 0.9379 (mmm) cc_final: 0.8884 (mmt) REVERT: E 358 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8110 (t) REVERT: A 305 MET cc_start: 0.9194 (mmm) cc_final: 0.8927 (tpp) REVERT: A 355 MET cc_start: 0.8893 (mmm) cc_final: 0.8673 (mmm) REVERT: D 227 MET cc_start: 0.9210 (tpp) cc_final: 0.8830 (tpp) REVERT: D 313 MET cc_start: 0.9516 (mmm) cc_final: 0.9105 (tpp) REVERT: G 5 ASP cc_start: 0.8706 (m-30) cc_final: 0.8356 (t0) REVERT: B 227 MET cc_start: 0.8849 (mmm) cc_final: 0.8164 (mpp) outliers start: 5 outliers final: 1 residues processed: 112 average time/residue: 0.2532 time to fit residues: 44.0261 Evaluate side-chains 112 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 1.781 ------------------------------------------------------------------------------- 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 61 optimal weight: 10.0000 chunk 165 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 152 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 GLN ** D 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 15460 Z= 0.367 Angle : 0.626 9.341 20960 Z= 0.304 Chirality : 0.045 0.142 2335 Planarity : 0.004 0.058 2670 Dihedral : 7.335 78.403 2145 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.37 % Allowed : 6.79 % Favored : 92.84 % 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: 1.09 (0.20), residues: 1885 helix: 1.11 (0.19), residues: 805 sheet: 0.25 (0.29), residues: 280 loop : 0.71 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.006 0.001 HIS D 88 PHE 0.012 0.001 PHE B 262 TYR 0.011 0.001 TYR A 306 ARG 0.005 0.000 ARG E 256 *********************** 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 fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 1.864 Fit side-chains REVERT: H 5 ASP cc_start: 0.9350 (m-30) cc_final: 0.9056 (t70) REVERT: C 123 MET cc_start: 0.9165 (tpp) cc_final: 0.8869 (tpp) REVERT: C 305 MET cc_start: 0.9048 (mmm) cc_final: 0.8827 (tpp) REVERT: C 325 MET cc_start: 0.8212 (ttp) cc_final: 0.7933 (ttm) REVERT: E 123 MET cc_start: 0.9094 (mmp) cc_final: 0.8727 (mmp) REVERT: E 132 MET cc_start: 0.8438 (tmm) cc_final: 0.8152 (tmm) REVERT: E 305 MET cc_start: 0.9355 (mmm) cc_final: 0.8854 (mmt) REVERT: E 358 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8162 (t) REVERT: A 227 MET cc_start: 0.9243 (mmm) cc_final: 0.8801 (mmm) REVERT: A 305 MET cc_start: 0.9192 (mmm) cc_final: 0.8919 (tpp) REVERT: A 355 MET cc_start: 0.8895 (mmm) cc_final: 0.8682 (mmp) REVERT: D 227 MET cc_start: 0.9214 (tpp) cc_final: 0.8782 (tpp) REVERT: D 283 MET cc_start: 0.9156 (mmm) cc_final: 0.8885 (mmm) REVERT: D 305 MET cc_start: 0.9150 (tpp) cc_final: 0.8697 (mmm) REVERT: D 313 MET cc_start: 0.9516 (mmm) cc_final: 0.9123 (tpp) REVERT: G 5 ASP cc_start: 0.8685 (m-30) cc_final: 0.8274 (t0) REVERT: B 227 MET cc_start: 0.8857 (mmm) cc_final: 0.8143 (mpp) outliers start: 6 outliers final: 2 residues processed: 113 average time/residue: 0.2759 time to fit residues: 48.3466 Evaluate side-chains 112 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain D residue 356 TRP Chi-restraints excluded: chain B residue 47 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 114 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 15460 Z= 0.245 Angle : 0.578 9.859 20960 Z= 0.276 Chirality : 0.044 0.139 2335 Planarity : 0.004 0.056 2670 Dihedral : 7.130 76.853 2145 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.31 % Allowed : 7.53 % Favored : 92.16 % 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: 1.39 (0.20), residues: 1885 helix: 1.47 (0.19), residues: 775 sheet: 0.22 (0.29), residues: 280 loop : 0.85 (0.24), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 79 HIS 0.004 0.001 HIS A 275 PHE 0.009 0.001 PHE D 255 TYR 0.011 0.001 TYR A 306 ARG 0.003 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 109 time to evaluate : 1.907 Fit side-chains revert: symmetry clash REVERT: H 5 ASP cc_start: 0.9301 (m-30) cc_final: 0.9010 (t70) REVERT: C 123 MET cc_start: 0.9151 (tpp) cc_final: 0.8856 (tpp) REVERT: C 305 MET cc_start: 0.9010 (mmm) cc_final: 0.8801 (tpp) REVERT: C 325 MET cc_start: 0.8176 (ttp) cc_final: 0.7886 (ttm) REVERT: E 123 MET cc_start: 0.9101 (mmp) cc_final: 0.8679 (mmt) REVERT: E 305 MET cc_start: 0.9367 (mmm) cc_final: 0.8849 (mmt) REVERT: E 358 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8271 (t) REVERT: A 305 MET cc_start: 0.9202 (mmm) cc_final: 0.8917 (tpp) REVERT: A 355 MET cc_start: 0.8870 (mmm) cc_final: 0.8651 (mmp) REVERT: D 227 MET cc_start: 0.9234 (tpp) cc_final: 0.8829 (tpp) REVERT: D 305 MET cc_start: 0.9116 (tpp) cc_final: 0.8682 (mmm) REVERT: D 313 MET cc_start: 0.9500 (mmm) cc_final: 0.9133 (tpp) REVERT: G 5 ASP cc_start: 0.8690 (m-30) cc_final: 0.8250 (t0) REVERT: B 227 MET cc_start: 0.8840 (mmm) cc_final: 0.8092 (mpp) outliers start: 5 outliers final: 1 residues processed: 112 average time/residue: 0.2567 time to fit residues: 44.5769 Evaluate side-chains 110 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 1.812 ------------------------------------------------------------------------------- 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 73 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 124 optimal weight: 0.4980 chunk 90 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 166 optimal weight: 0.4980 chunk 175 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15460 Z= 0.149 Angle : 0.560 12.267 20960 Z= 0.262 Chirality : 0.043 0.139 2335 Planarity : 0.004 0.057 2670 Dihedral : 6.843 77.254 2145 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.19 % Allowed : 7.78 % Favored : 92.04 % 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: 1.47 (0.20), residues: 1885 helix: 1.43 (0.19), residues: 800 sheet: 0.29 (0.30), residues: 280 loop : 0.98 (0.24), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 356 HIS 0.003 0.001 HIS A 275 PHE 0.009 0.001 PHE D 255 TYR 0.014 0.001 TYR D 306 ARG 0.003 0.000 ARG A 206 *********************** 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 112 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.722 Fit side-chains revert: symmetry clash REVERT: H 5 ASP cc_start: 0.9281 (m-30) cc_final: 0.9025 (t70) REVERT: C 123 MET cc_start: 0.9119 (tpp) cc_final: 0.8794 (tpp) REVERT: C 313 MET cc_start: 0.9339 (mmm) cc_final: 0.8800 (tpt) REVERT: C 325 MET cc_start: 0.8019 (ttp) cc_final: 0.7792 (ttm) REVERT: E 123 MET cc_start: 0.9103 (mmp) cc_final: 0.8854 (mmt) REVERT: E 132 MET cc_start: 0.8394 (tmm) cc_final: 0.8188 (tmm) REVERT: E 305 MET cc_start: 0.9392 (mmm) cc_final: 0.8884 (mmt) REVERT: E 358 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8264 (t) REVERT: A 227 MET cc_start: 0.9237 (mmm) cc_final: 0.8810 (mmm) REVERT: A 299 MET cc_start: 0.8597 (mmm) cc_final: 0.8351 (mtp) REVERT: A 305 MET cc_start: 0.9156 (mmm) cc_final: 0.8863 (tpp) REVERT: A 355 MET cc_start: 0.8834 (mmm) cc_final: 0.8607 (mmm) REVERT: D 227 MET cc_start: 0.9195 (tpp) cc_final: 0.8835 (tpp) REVERT: D 305 MET cc_start: 0.9031 (tpp) cc_final: 0.8630 (mmm) REVERT: D 313 MET cc_start: 0.9488 (mmm) cc_final: 0.9126 (tpp) REVERT: G 5 ASP cc_start: 0.8809 (m-30) cc_final: 0.8334 (t0) REVERT: B 227 MET cc_start: 0.8832 (mmm) cc_final: 0.8058 (mpp) REVERT: B 299 MET cc_start: 0.8880 (mmm) cc_final: 0.8328 (mmm) outliers start: 3 outliers final: 2 residues processed: 111 average time/residue: 0.2587 time to fit residues: 45.0777 Evaluate side-chains 112 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain B residue 47 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 8.9990 chunk 170 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3209 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= 0.249 Angle : 0.589 9.765 20960 Z= 0.276 Chirality : 0.044 0.138 2335 Planarity : 0.004 0.055 2670 Dihedral : 6.880 77.338 2145 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.19 % Allowed : 8.02 % Favored : 91.79 % 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: 1.19 (0.20), residues: 1885 helix: 1.14 (0.19), residues: 845 sheet: 0.30 (0.30), residues: 280 loop : 0.81 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 79 HIS 0.004 0.001 HIS A 275 PHE 0.009 0.001 PHE D 255 TYR 0.008 0.001 TYR A 306 ARG 0.004 0.000 ARG D 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.646 Fit side-chains revert: symmetry clash REVERT: H 5 ASP cc_start: 0.9292 (m-30) cc_final: 0.9061 (t70) REVERT: C 325 MET cc_start: 0.8233 (ttp) cc_final: 0.8004 (ttm) REVERT: E 123 MET cc_start: 0.9113 (mmp) cc_final: 0.8689 (mmt) REVERT: E 132 MET cc_start: 0.8434 (tmm) cc_final: 0.8177 (tmm) REVERT: E 305 MET cc_start: 0.9367 (mmm) cc_final: 0.8838 (mmt) REVERT: E 358 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8219 (t) REVERT: A 132 MET cc_start: 0.8485 (tmm) cc_final: 0.8283 (tmm) REVERT: A 227 MET cc_start: 0.9240 (mmm) cc_final: 0.8800 (mmm) REVERT: A 283 MET cc_start: 0.9339 (mmm) cc_final: 0.9108 (mmm) REVERT: A 305 MET cc_start: 0.9207 (mmm) cc_final: 0.8912 (tpp) REVERT: A 355 MET cc_start: 0.8863 (mmm) cc_final: 0.8625 (mmm) REVERT: D 227 MET cc_start: 0.9214 (tpp) cc_final: 0.8804 (tpp) REVERT: D 305 MET cc_start: 0.9144 (tpp) cc_final: 0.8699 (mmm) REVERT: D 313 MET cc_start: 0.9505 (mmm) cc_final: 0.9101 (tpp) REVERT: G 5 ASP cc_start: 0.8781 (m-30) cc_final: 0.8254 (t0) REVERT: B 227 MET cc_start: 0.8856 (mmm) cc_final: 0.8079 (mpp) REVERT: B 299 MET cc_start: 0.8921 (mmm) cc_final: 0.8265 (mmm) outliers start: 3 outliers final: 2 residues processed: 111 average time/residue: 0.2526 time to fit residues: 43.7498 Evaluate side-chains 110 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain B residue 47 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 150 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN E 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 15460 Z= 0.322 Angle : 0.626 9.417 20960 Z= 0.297 Chirality : 0.045 0.140 2335 Planarity : 0.004 0.053 2670 Dihedral : 7.021 77.940 2145 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.25 % Allowed : 8.21 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.20), residues: 1885 helix: 1.26 (0.19), residues: 815 sheet: 0.20 (0.30), residues: 280 loop : 0.79 (0.24), residues: 790 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 B 262 TYR 0.010 0.001 TYR E 279 ARG 0.004 0.000 ARG D 335 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 1.735 Fit side-chains revert: symmetry clash REVERT: H 5 ASP cc_start: 0.9305 (m-30) cc_final: 0.9071 (t70) REVERT: C 313 MET cc_start: 0.9387 (mmm) cc_final: 0.8751 (tpp) REVERT: C 325 MET cc_start: 0.8294 (ttp) cc_final: 0.8026 (ttm) REVERT: E 123 MET cc_start: 0.9121 (mmp) cc_final: 0.8682 (mmt) REVERT: E 132 MET cc_start: 0.8435 (tmm) cc_final: 0.8157 (tmm) REVERT: E 305 MET cc_start: 0.9342 (mmm) cc_final: 0.8827 (mmt) REVERT: E 358 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8244 (t) REVERT: A 227 MET cc_start: 0.9237 (mmm) cc_final: 0.8797 (mmm) REVERT: A 283 MET cc_start: 0.9315 (mmm) cc_final: 0.9081 (mmm) REVERT: A 305 MET cc_start: 0.9214 (mmm) cc_final: 0.8898 (tpp) REVERT: A 355 MET cc_start: 0.8868 (mmm) cc_final: 0.8625 (mmm) REVERT: D 227 MET cc_start: 0.9231 (tpp) cc_final: 0.8784 (tpp) REVERT: D 305 MET cc_start: 0.9177 (tpp) cc_final: 0.8726 (mmm) REVERT: D 313 MET cc_start: 0.9507 (mmm) cc_final: 0.9119 (tpp) REVERT: G 5 ASP cc_start: 0.8900 (m-30) cc_final: 0.8401 (t70) REVERT: B 227 MET cc_start: 0.8865 (mmm) cc_final: 0.8085 (mpp) REVERT: B 299 MET cc_start: 0.8971 (mmm) cc_final: 0.8328 (mmm) outliers start: 4 outliers final: 3 residues processed: 109 average time/residue: 0.2627 time to fit residues: 44.2020 Evaluate side-chains 110 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 46 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 150 optimal weight: 0.4980 chunk 63 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.2888 r_free = 0.2888 target = 0.034021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.028233 restraints weight = 101938.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.029421 restraints weight = 49286.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.030255 restraints weight = 30139.434| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3337 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= 0.150 Angle : 0.567 9.074 20960 Z= 0.263 Chirality : 0.043 0.137 2335 Planarity : 0.004 0.056 2670 Dihedral : 6.729 77.892 2145 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.25 % Allowed : 8.21 % Favored : 91.54 % 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: 1.46 (0.19), residues: 805 sheet: 0.28 (0.30), residues: 280 loop : 0.92 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 356 HIS 0.003 0.001 HIS A 275 PHE 0.011 0.001 PHE D 255 TYR 0.015 0.001 TYR D 306 ARG 0.003 0.000 ARG C 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2181.70 seconds wall clock time: 40 minutes 52.29 seconds (2452.29 seconds total)