Starting phenix.real_space_refine on Wed Mar 4 02:47:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnr_27577/03_2026/8dnr_27577_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnr_27577/03_2026/8dnr_27577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dnr_27577/03_2026/8dnr_27577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnr_27577/03_2026/8dnr_27577.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnr_27577/03_2026/8dnr_27577_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnr_27577/03_2026/8dnr_27577_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.074 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 6459 2.51 5 N 1641 2.21 5 O 2031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10191 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3341 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3341 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3341 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.58, per 1000 atoms: 0.25 Number of scatterers: 10191 At special positions: 0 Unit cell: (101.52, 102.46, 104.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 2031 8.00 N 1641 7.00 C 6459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 104 " - pdb=" SG CYS E 114 " distance=2.02 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 340 " distance=2.03 Simple disulfide: pdb=" SG CYS E 355 " - pdb=" SG CYS E 363 " distance=2.03 Simple disulfide: pdb=" SG CYS E 387 " - pdb=" SG CYS E 392 " distance=2.03 Simple disulfide: pdb=" SG CYS E 394 " - pdb=" SG CYS E 417 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 99 " " NAG A 602 " - " ASN A 67 " " NAG A 603 " - " ASN A 414 " " NAG A 604 " - " ASN A 464 " " NAG B 601 " - " ASN B 99 " " NAG B 602 " - " ASN B 67 " " NAG B 603 " - " ASN B 414 " " NAG B 604 " - " ASN B 464 " " NAG E 601 " - " ASN E 99 " " NAG E 602 " - " ASN E 67 " " NAG E 603 " - " ASN E 464 " " NAG E 604 " - " ASN E 414 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 482.1 milliseconds 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 15 sheets defined 38.7% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 29 through 36 removed outlier: 3.504A pdb=" N ILE A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.550A pdb=" N CYS A 71 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 68 through 72' Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.549A pdb=" N GLY A 85 " --> pdb=" O SER A 81 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 3.655A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.949A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 175 through 183 Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.692A pdb=" N THR A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 349 through 358 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 452 through 471 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.803A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 removed outlier: 3.567A pdb=" N CYS B 71 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 72 " --> pdb=" O SER B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 68 through 72' Processing helix chain 'B' and resid 74 through 99 removed outlier: 3.583A pdb=" N GLY B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Proline residue: B 89 - end of helix removed outlier: 3.712A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.976A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 153 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 191 through 215 removed outlier: 3.737A pdb=" N THR B 195 " --> pdb=" O PRO B 191 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 452 through 471 removed outlier: 3.917A pdb=" N GLN B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 36 removed outlier: 3.593A pdb=" N ILE E 36 " --> pdb=" O LYS E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 72 removed outlier: 3.535A pdb=" N CYS E 71 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR E 72 " --> pdb=" O SER E 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 68 through 72' Processing helix chain 'E' and resid 74 through 99 removed outlier: 3.553A pdb=" N GLY E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Proline residue: E 89 - end of helix removed outlier: 3.686A pdb=" N TYR E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'E' and resid 125 through 145 removed outlier: 3.959A pdb=" N LYS E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 153 Processing helix chain 'E' and resid 175 through 183 Processing helix chain 'E' and resid 191 through 215 removed outlier: 3.703A pdb=" N THR E 195 " --> pdb=" O PRO E 191 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL E 213 " --> pdb=" O ASP E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 233 through 236 Processing helix chain 'E' and resid 238 through 247 Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 328 through 331 Processing helix chain 'E' and resid 349 through 357 Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 452 through 471 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 11.275A pdb=" N TYR A 170 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASP A 56 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N PHE A 172 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL A 58 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LYS A 40 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU A 297 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE A 42 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 46 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 291 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N ILE A 48 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N GLN A 289 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 10.064A pdb=" N SER A 50 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N GLU A 287 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 10.659A pdb=" N LEU A 285 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N THR A 54 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 9.890A pdb=" N ASP A 56 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N TYR A 281 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N VAL A 58 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N ARG A 279 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N LYS A 60 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 9.938A pdb=" N ILE A 277 " --> pdb=" O LYS A 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 298 current: chain 'A' and resid 332 through 333 Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 270 removed outlier: 3.659A pdb=" N ALA A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE A 277 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 9.938A pdb=" N ILE A 277 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N LYS A 60 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 9.530A pdb=" N ARG A 279 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 9.687A pdb=" N VAL A 58 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 9.658A pdb=" N TYR A 281 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 9.890A pdb=" N ASP A 56 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N THR A 54 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 10.659A pdb=" N LEU A 285 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N GLU A 287 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 10.064A pdb=" N SER A 50 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 9.572A pdb=" N GLN A 289 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 10.706A pdb=" N ILE A 48 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 291 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 46 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE A 42 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N LEU A 297 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LYS A 40 " --> pdb=" O LEU A 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 322 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 4.554A pdb=" N CYS B 392 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 303 removed outlier: 5.965A pdb=" N ARG A 365 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 400 through 401 removed outlier: 4.546A pdb=" N CYS A 392 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE A 426 " --> pdb=" O MET E 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 158 through 162 removed outlier: 17.146A pdb=" N THR B 168 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 11.821A pdb=" N THR B 54 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 11.318A pdb=" N TYR B 170 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ASP B 56 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N PHE B 172 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 58 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LYS B 40 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU B 297 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE B 42 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR B 46 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 291 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 10.690A pdb=" N ILE B 48 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N GLN B 289 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N SER B 50 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N GLU B 287 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 10.631A pdb=" N LEU B 285 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N THR B 54 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N ASP B 56 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N TYR B 281 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 9.669A pdb=" N VAL B 58 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N ARG B 279 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N LYS B 60 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ILE B 277 " --> pdb=" O LYS B 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 275 through 297 current: chain 'B' and resid 332 through 333 Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 270 removed outlier: 3.625A pdb=" N ALA B 263 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 277 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ILE B 277 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 9.696A pdb=" N LYS B 60 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N ARG B 279 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 9.669A pdb=" N VAL B 58 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N TYR B 281 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 10.245A pdb=" N ASP B 56 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N THR B 54 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 10.631A pdb=" N LEU B 285 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N GLU B 287 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N SER B 50 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N GLN B 289 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 10.690A pdb=" N ILE B 48 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 291 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR B 46 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE B 42 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU B 297 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LYS B 40 " --> pdb=" O LEU B 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 39 through 60 current: chain 'B' and resid 322 through 326 Processing sheet with id=AB1, first strand: chain 'B' and resid 101 through 102 removed outlier: 4.517A pdb=" N CYS E 392 " --> pdb=" O ILE E 401 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AB3, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AB4, first strand: chain 'E' and resid 158 through 162 removed outlier: 17.107A pdb=" N THR E 168 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 11.769A pdb=" N THR E 54 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 11.275A pdb=" N TYR E 170 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ASP E 56 " --> pdb=" O TYR E 170 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N PHE E 172 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL E 58 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS E 40 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU E 297 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE E 42 " --> pdb=" O GLU E 295 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR E 46 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA E 291 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 10.713A pdb=" N ILE E 48 " --> pdb=" O GLN E 289 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N GLN E 289 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 10.264A pdb=" N SER E 50 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N GLU E 287 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N LEU E 285 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N THR E 54 " --> pdb=" O PRO E 283 " (cutoff:3.500A) removed outlier: 9.977A pdb=" N ASP E 56 " --> pdb=" O TYR E 281 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N TYR E 281 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N VAL E 58 " --> pdb=" O ARG E 279 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ARG E 279 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N LYS E 60 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N ILE E 277 " --> pdb=" O LYS E 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 275 through 298 current: chain 'E' and resid 332 through 333 Processing sheet with id=AB5, first strand: chain 'E' and resid 263 through 270 removed outlier: 6.539A pdb=" N ILE E 277 " --> pdb=" O VAL E 267 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL E 269 " --> pdb=" O TYR E 275 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N TYR E 275 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N ILE E 277 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N LYS E 60 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N ARG E 279 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 9.740A pdb=" N VAL E 58 " --> pdb=" O ARG E 279 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N TYR E 281 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 9.977A pdb=" N ASP E 56 " --> pdb=" O TYR E 281 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N THR E 54 " --> pdb=" O PRO E 283 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N LEU E 285 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 9.444A pdb=" N GLU E 287 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 10.264A pdb=" N SER E 50 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N GLN E 289 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 10.713A pdb=" N ILE E 48 " --> pdb=" O GLN E 289 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA E 291 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR E 46 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE E 42 " --> pdb=" O GLU E 295 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU E 297 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS E 40 " --> pdb=" O LEU E 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 38 through 60 current: chain 'E' and resid 322 through 326 Processing sheet with id=AB6, first strand: chain 'E' and resid 301 through 303 418 hydrogen bonds defined for protein. 1164 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: 1.68 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3251 1.34 - 1.47: 2255 1.47 - 1.59: 4745 1.59 - 1.72: 0 1.72 - 1.84: 84 Bond restraints: 10335 Sorted by residual: bond pdb=" N GLY E 430 " pdb=" CA GLY E 430 " ideal model delta sigma weight residual 1.445 1.476 -0.032 9.90e-03 1.02e+04 1.04e+01 bond pdb=" N LEU E 429 " pdb=" CA LEU E 429 " ideal model delta sigma weight residual 1.452 1.490 -0.037 1.22e-02 6.72e+03 9.42e+00 bond pdb=" N ILE B 118 " pdb=" CA ILE B 118 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.30e-02 5.92e+03 7.35e+00 bond pdb=" N LYS E 431 " pdb=" CA LYS E 431 " ideal model delta sigma weight residual 1.456 1.488 -0.033 1.25e-02 6.40e+03 6.85e+00 bond pdb=" N TYR E 432 " pdb=" CA TYR E 432 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.33e-02 5.65e+03 6.38e+00 ... (remaining 10330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 13775 1.64 - 3.29: 242 3.29 - 4.93: 37 4.93 - 6.57: 0 6.57 - 8.22: 1 Bond angle restraints: 14055 Sorted by residual: angle pdb=" N THR E 415 " pdb=" CA THR E 415 " pdb=" C THR E 415 " ideal model delta sigma weight residual 111.28 107.24 4.04 1.09e+00 8.42e-01 1.38e+01 angle pdb=" CA MET B 463 " pdb=" C MET B 463 " pdb=" N ASN B 464 " ideal model delta sigma weight residual 117.30 121.49 -4.19 1.16e+00 7.43e-01 1.30e+01 angle pdb=" CA CYS E 104 " pdb=" CB CYS E 104 " pdb=" SG CYS E 104 " ideal model delta sigma weight residual 114.40 122.62 -8.22 2.30e+00 1.89e-01 1.28e+01 angle pdb=" CA GLY E 430 " pdb=" C GLY E 430 " pdb=" O GLY E 430 " ideal model delta sigma weight residual 121.57 117.91 3.66 1.07e+00 8.73e-01 1.17e+01 angle pdb=" N ASN E 414 " pdb=" CA ASN E 414 " pdb=" C ASN E 414 " ideal model delta sigma weight residual 112.89 108.76 4.13 1.24e+00 6.50e-01 1.11e+01 ... (remaining 14050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.24: 5742 16.24 - 32.48: 512 32.48 - 48.72: 178 48.72 - 64.96: 69 64.96 - 81.19: 12 Dihedral angle restraints: 6513 sinusoidal: 2655 harmonic: 3858 Sorted by residual: dihedral pdb=" CB CYS A 71 " pdb=" SG CYS A 71 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -156.11 70.11 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CB CYS B 71 " pdb=" SG CYS B 71 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual -86.00 -146.68 60.68 1 1.00e+01 1.00e-02 4.90e+01 dihedral pdb=" CB CYS E 71 " pdb=" SG CYS E 71 " pdb=" SG CYS E 192 " pdb=" CB CYS E 192 " ideal model delta sinusoidal sigma weight residual -86.00 -144.18 58.18 1 1.00e+01 1.00e-02 4.54e+01 ... (remaining 6510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1069 0.030 - 0.061: 406 0.061 - 0.091: 141 0.091 - 0.121: 144 0.121 - 0.151: 13 Chirality restraints: 1773 Sorted by residual: chirality pdb=" CB ILE B 118 " pdb=" CA ILE B 118 " pdb=" CG1 ILE B 118 " pdb=" CG2 ILE B 118 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA LEU E 429 " pdb=" N LEU E 429 " pdb=" C LEU E 429 " pdb=" CB LEU E 429 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE A 426 " pdb=" N ILE A 426 " pdb=" C ILE A 426 " pdb=" CB ILE A 426 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 1770 not shown) Planarity restraints: 1761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 604 " -0.044 2.00e-02 2.50e+03 3.70e-02 1.71e+01 pdb=" C7 NAG E 604 " 0.015 2.00e-02 2.50e+03 pdb=" C8 NAG E 604 " 0.011 2.00e-02 2.50e+03 pdb=" N2 NAG E 604 " 0.056 2.00e-02 2.50e+03 pdb=" O7 NAG E 604 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 74 " 0.008 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C THR E 74 " -0.030 2.00e-02 2.50e+03 pdb=" O THR E 74 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL E 75 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 413 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C ASP E 413 " -0.028 2.00e-02 2.50e+03 pdb=" O ASP E 413 " 0.010 2.00e-02 2.50e+03 pdb=" N ASN E 414 " 0.010 2.00e-02 2.50e+03 ... (remaining 1758 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 53 2.57 - 3.16: 8105 3.16 - 3.74: 15673 3.74 - 4.32: 23119 4.32 - 4.90: 37980 Nonbonded interactions: 84930 Sorted by model distance: nonbonded pdb=" CG LYS B 55 " pdb=" OH TYR B 248 " model vdw 1.992 3.440 nonbonded pdb=" CD LYS B 55 " pdb=" OH TYR B 248 " model vdw 2.152 3.440 nonbonded pdb=" OG SER A 458 " pdb=" OG SER E 351 " model vdw 2.187 3.040 nonbonded pdb=" OD1 ASN E 64 " pdb=" OG SER E 66 " model vdw 2.221 3.040 nonbonded pdb=" OG SER B 351 " pdb=" OG SER E 458 " model vdw 2.227 3.040 ... (remaining 84925 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.510 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 0.037 10365 Z= 0.167 Angle : 0.532 8.218 14127 Z= 0.292 Chirality : 0.045 0.151 1773 Planarity : 0.003 0.039 1749 Dihedral : 15.267 81.194 3969 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.38 % Favored : 97.54 % Rotamer: Outliers : 1.47 % Allowed : 15.15 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.23), residues: 1302 helix: 1.39 (0.26), residues: 432 sheet: 0.43 (0.32), residues: 258 loop : -0.56 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 244 TYR 0.009 0.001 TYR E 432 PHE 0.007 0.001 PHE B 301 TRP 0.002 0.000 TRP A 308 HIS 0.004 0.001 HIS E 102 Details of bonding type rmsd covalent geometry : bond 0.00324 (10335) covalent geometry : angle 0.52057 (14055) SS BOND : bond 0.00240 ( 18) SS BOND : angle 1.38602 ( 36) hydrogen bonds : bond 0.15156 ( 409) hydrogen bonds : angle 6.52912 ( 1164) link_NAG-ASN : bond 0.00167 ( 12) link_NAG-ASN : angle 1.80904 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.395 Fit side-chains REVERT: A 95 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7579 (mm-30) REVERT: E 250 THR cc_start: 0.7512 (m) cc_final: 0.6775 (t) outliers start: 17 outliers final: 13 residues processed: 131 average time/residue: 0.4489 time to fit residues: 64.4779 Evaluate side-chains 118 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 371 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 303 ASN A 314 ASN B 314 ASN E 102 HIS E 194 GLN E 314 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.115746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.093243 restraints weight = 11431.506| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.85 r_work: 0.2881 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.0671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10365 Z= 0.127 Angle : 0.488 4.786 14127 Z= 0.255 Chirality : 0.046 0.154 1773 Planarity : 0.003 0.037 1749 Dihedral : 7.234 59.810 1667 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.20 % Allowed : 12.90 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1302 helix: 1.56 (0.25), residues: 447 sheet: 0.26 (0.31), residues: 258 loop : -0.31 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.019 0.001 TYR B 248 PHE 0.010 0.001 PHE B 301 TRP 0.003 0.001 TRP B 308 HIS 0.002 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00308 (10335) covalent geometry : angle 0.47635 (14055) SS BOND : bond 0.00187 ( 18) SS BOND : angle 1.37876 ( 36) hydrogen bonds : bond 0.03567 ( 409) hydrogen bonds : angle 4.80646 ( 1164) link_NAG-ASN : bond 0.00137 ( 12) link_NAG-ASN : angle 1.74647 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.385 Fit side-chains REVERT: A 95 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7741 (mm-30) REVERT: A 335 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8739 (mptp) REVERT: B 220 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.7980 (m-30) REVERT: E 335 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8690 (mptp) outliers start: 37 outliers final: 10 residues processed: 138 average time/residue: 0.4037 time to fit residues: 61.5429 Evaluate side-chains 121 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 335 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 96 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 140 ASN B 314 ASN E 140 ASN E 314 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.114110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.091660 restraints weight = 11396.306| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.84 r_work: 0.2800 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10365 Z= 0.183 Angle : 0.541 5.156 14127 Z= 0.279 Chirality : 0.047 0.147 1773 Planarity : 0.004 0.039 1749 Dihedral : 6.661 58.157 1648 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.64 % Allowed : 12.90 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.22), residues: 1302 helix: 1.46 (0.25), residues: 441 sheet: 0.22 (0.31), residues: 258 loop : -0.41 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 244 TYR 0.014 0.002 TYR B 275 PHE 0.011 0.001 PHE B 301 TRP 0.003 0.001 TRP A 308 HIS 0.003 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00458 (10335) covalent geometry : angle 0.52456 (14055) SS BOND : bond 0.00169 ( 18) SS BOND : angle 1.82977 ( 36) hydrogen bonds : bond 0.03874 ( 409) hydrogen bonds : angle 4.77436 ( 1164) link_NAG-ASN : bond 0.00137 ( 12) link_NAG-ASN : angle 1.97474 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 0.427 Fit side-chains REVERT: A 95 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7766 (mm-30) REVERT: A 335 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8698 (mptp) REVERT: E 335 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8679 (mptp) outliers start: 42 outliers final: 16 residues processed: 128 average time/residue: 0.4582 time to fit residues: 64.4332 Evaluate side-chains 121 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 335 LYS Chi-restraints excluded: chain E residue 415 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 55 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 140 ASN B 314 ASN E 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.114462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.091804 restraints weight = 11581.537| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.86 r_work: 0.2827 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10365 Z= 0.106 Angle : 0.468 4.741 14127 Z= 0.243 Chirality : 0.045 0.148 1773 Planarity : 0.003 0.038 1749 Dihedral : 6.068 54.739 1648 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.46 % Allowed : 12.81 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.23), residues: 1302 helix: 1.69 (0.25), residues: 447 sheet: 0.21 (0.31), residues: 258 loop : -0.25 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 375 TYR 0.007 0.001 TYR E 438 PHE 0.007 0.001 PHE B 301 TRP 0.002 0.001 TRP B 308 HIS 0.001 0.000 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00255 (10335) covalent geometry : angle 0.45397 (14055) SS BOND : bond 0.00143 ( 18) SS BOND : angle 1.41712 ( 36) hydrogen bonds : bond 0.02970 ( 409) hydrogen bonds : angle 4.48365 ( 1164) link_NAG-ASN : bond 0.00139 ( 12) link_NAG-ASN : angle 1.82102 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.402 Fit side-chains REVERT: A 95 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 335 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8671 (mptp) REVERT: E 335 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8723 (mptp) outliers start: 40 outliers final: 15 residues processed: 126 average time/residue: 0.4828 time to fit residues: 66.7831 Evaluate side-chains 120 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 335 LYS Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 436 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 9 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 126 optimal weight: 0.0970 chunk 44 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 140 ASN B 314 ASN E 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.114694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.092202 restraints weight = 11470.222| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.85 r_work: 0.2815 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10365 Z= 0.130 Angle : 0.489 4.730 14127 Z= 0.252 Chirality : 0.045 0.142 1773 Planarity : 0.003 0.038 1749 Dihedral : 5.902 55.276 1648 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.12 % Allowed : 13.51 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.23), residues: 1302 helix: 1.68 (0.25), residues: 447 sheet: 0.22 (0.31), residues: 258 loop : -0.23 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 244 TYR 0.010 0.001 TYR B 275 PHE 0.009 0.001 PHE B 301 TRP 0.002 0.001 TRP B 308 HIS 0.001 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00320 (10335) covalent geometry : angle 0.47540 (14055) SS BOND : bond 0.00229 ( 18) SS BOND : angle 1.43457 ( 36) hydrogen bonds : bond 0.03130 ( 409) hydrogen bonds : angle 4.49885 ( 1164) link_NAG-ASN : bond 0.00137 ( 12) link_NAG-ASN : angle 1.84103 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 105 time to evaluate : 0.444 Fit side-chains REVERT: A 95 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7773 (mm-30) REVERT: A 335 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8621 (mptp) REVERT: A 422 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7923 (mt) REVERT: E 96 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8247 (tm) REVERT: E 335 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8679 (mptp) outliers start: 36 outliers final: 15 residues processed: 125 average time/residue: 0.4631 time to fit residues: 63.6968 Evaluate side-chains 120 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 335 LYS Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 436 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 34 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 120 optimal weight: 0.5980 chunk 19 optimal weight: 0.2980 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 140 ASN B 314 ASN E 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.093430 restraints weight = 11555.576| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.86 r_work: 0.2834 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10365 Z= 0.101 Angle : 0.459 4.735 14127 Z= 0.238 Chirality : 0.044 0.142 1773 Planarity : 0.003 0.037 1749 Dihedral : 5.171 53.465 1645 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.12 % Allowed : 13.59 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.23), residues: 1302 helix: 1.85 (0.25), residues: 447 sheet: 0.24 (0.31), residues: 258 loop : -0.18 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 244 TYR 0.007 0.001 TYR A 438 PHE 0.007 0.001 PHE B 301 TRP 0.002 0.001 TRP A 308 HIS 0.002 0.000 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00238 (10335) covalent geometry : angle 0.44667 (14055) SS BOND : bond 0.00160 ( 18) SS BOND : angle 1.32297 ( 36) hydrogen bonds : bond 0.02809 ( 409) hydrogen bonds : angle 4.35191 ( 1164) link_NAG-ASN : bond 0.00139 ( 12) link_NAG-ASN : angle 1.75868 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 107 time to evaluate : 0.401 Fit side-chains REVERT: A 95 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7666 (mt-10) REVERT: A 335 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8627 (mptp) REVERT: A 422 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7925 (mt) REVERT: B 210 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8076 (tt) REVERT: B 220 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8007 (m-30) REVERT: E 96 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8245 (tm) REVERT: E 335 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8615 (mptp) outliers start: 36 outliers final: 15 residues processed: 126 average time/residue: 0.4277 time to fit residues: 59.5593 Evaluate side-chains 126 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 335 LYS Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain E residue 436 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 120 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 140 ASN B 314 ASN E 102 HIS E 314 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.115012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.092409 restraints weight = 11365.599| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.85 r_work: 0.2793 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10365 Z= 0.164 Angle : 0.532 6.996 14127 Z= 0.271 Chirality : 0.046 0.143 1773 Planarity : 0.003 0.038 1749 Dihedral : 5.395 54.412 1645 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.94 % Allowed : 14.37 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.23), residues: 1302 helix: 1.66 (0.25), residues: 447 sheet: 0.20 (0.31), residues: 258 loop : -0.23 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 244 TYR 0.013 0.002 TYR B 275 PHE 0.011 0.001 PHE B 301 TRP 0.003 0.001 TRP A 308 HIS 0.004 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00409 (10335) covalent geometry : angle 0.51280 (14055) SS BOND : bond 0.00218 ( 18) SS BOND : angle 2.25873 ( 36) hydrogen bonds : bond 0.03394 ( 409) hydrogen bonds : angle 4.50822 ( 1164) link_NAG-ASN : bond 0.00153 ( 12) link_NAG-ASN : angle 1.85844 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 0.393 Fit side-chains REVERT: A 95 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7795 (mm-30) REVERT: A 335 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8575 (mptp) REVERT: A 422 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7950 (mt) REVERT: B 210 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8118 (tt) REVERT: E 96 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8274 (tm) REVERT: E 335 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8667 (mptp) outliers start: 34 outliers final: 15 residues processed: 123 average time/residue: 0.4432 time to fit residues: 60.0909 Evaluate side-chains 121 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 335 LYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 436 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 140 ASN B 314 ASN E 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.115489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.092869 restraints weight = 11395.408| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.85 r_work: 0.2812 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10365 Z= 0.136 Angle : 0.508 5.910 14127 Z= 0.261 Chirality : 0.046 0.140 1773 Planarity : 0.003 0.038 1749 Dihedral : 5.289 53.982 1645 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.16 % Allowed : 15.24 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.23), residues: 1302 helix: 1.71 (0.25), residues: 447 sheet: 0.19 (0.31), residues: 258 loop : -0.20 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 375 TYR 0.010 0.001 TYR B 275 PHE 0.009 0.001 PHE B 301 TRP 0.002 0.001 TRP A 308 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00335 (10335) covalent geometry : angle 0.49180 (14055) SS BOND : bond 0.00155 ( 18) SS BOND : angle 1.85879 ( 36) hydrogen bonds : bond 0.03149 ( 409) hydrogen bonds : angle 4.48956 ( 1164) link_NAG-ASN : bond 0.00133 ( 12) link_NAG-ASN : angle 1.83393 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.384 Fit side-chains REVERT: A 95 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7734 (mm-30) REVERT: A 335 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8591 (mptp) REVERT: A 422 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7925 (mt) REVERT: B 210 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8059 (tt) REVERT: E 96 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8249 (tm) REVERT: E 335 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8649 (mptp) outliers start: 25 outliers final: 18 residues processed: 119 average time/residue: 0.4695 time to fit residues: 61.3312 Evaluate side-chains 126 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 335 LYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 436 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 86 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 chunk 112 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 140 ASN B 314 ASN E 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.093593 restraints weight = 11298.891| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.84 r_work: 0.2809 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10365 Z= 0.108 Angle : 0.479 6.400 14127 Z= 0.245 Chirality : 0.045 0.142 1773 Planarity : 0.003 0.038 1749 Dihedral : 5.085 53.408 1645 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.16 % Allowed : 15.32 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.23), residues: 1302 helix: 1.84 (0.25), residues: 447 sheet: 0.22 (0.31), residues: 258 loop : -0.15 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 375 TYR 0.011 0.001 TYR B 248 PHE 0.008 0.001 PHE B 301 TRP 0.002 0.001 TRP E 308 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00259 (10335) covalent geometry : angle 0.46475 (14055) SS BOND : bond 0.00153 ( 18) SS BOND : angle 1.61124 ( 36) hydrogen bonds : bond 0.02879 ( 409) hydrogen bonds : angle 4.36308 ( 1164) link_NAG-ASN : bond 0.00143 ( 12) link_NAG-ASN : angle 1.74492 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.348 Fit side-chains REVERT: A 95 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7781 (mm-30) REVERT: A 335 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8567 (mptp) REVERT: A 422 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7966 (mt) REVERT: B 103 ASP cc_start: 0.7152 (p0) cc_final: 0.6662 (t0) REVERT: B 210 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8035 (tt) REVERT: B 220 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.7930 (m-30) REVERT: E 96 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8256 (tm) REVERT: E 335 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8634 (mptp) outliers start: 25 outliers final: 16 residues processed: 120 average time/residue: 0.4635 time to fit residues: 61.0801 Evaluate side-chains 125 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 335 LYS Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 436 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 37 optimal weight: 0.0030 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 83 optimal weight: 0.0030 chunk 82 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 19 optimal weight: 0.2980 overall best weight: 0.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 140 ASN B 314 ASN E 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.119687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.097224 restraints weight = 11239.563| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.85 r_work: 0.2883 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10365 Z= 0.084 Angle : 0.454 7.121 14127 Z= 0.233 Chirality : 0.044 0.142 1773 Planarity : 0.003 0.037 1749 Dihedral : 4.830 53.046 1645 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.82 % Allowed : 15.76 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.23), residues: 1302 helix: 2.37 (0.27), residues: 411 sheet: 0.31 (0.31), residues: 258 loop : -0.18 (0.23), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 244 TYR 0.013 0.001 TYR B 248 PHE 0.006 0.001 PHE A 376 TRP 0.002 0.001 TRP B 308 HIS 0.002 0.000 HIS E 372 Details of bonding type rmsd covalent geometry : bond 0.00189 (10335) covalent geometry : angle 0.44245 (14055) SS BOND : bond 0.00149 ( 18) SS BOND : angle 1.34960 ( 36) hydrogen bonds : bond 0.02504 ( 409) hydrogen bonds : angle 4.18276 ( 1164) link_NAG-ASN : bond 0.00148 ( 12) link_NAG-ASN : angle 1.62590 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.344 Fit side-chains REVERT: A 95 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7661 (mt-10) REVERT: A 335 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8587 (mptp) REVERT: A 422 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7921 (mt) REVERT: B 103 ASP cc_start: 0.7107 (p0) cc_final: 0.6630 (m-30) REVERT: B 220 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: B 427 ILE cc_start: 0.8487 (mt) cc_final: 0.8125 (tp) outliers start: 21 outliers final: 11 residues processed: 123 average time/residue: 0.4391 time to fit residues: 59.5818 Evaluate side-chains 124 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 335 LYS Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 436 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 ASN A 314 ASN B 140 ASN B 314 ASN E 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.095604 restraints weight = 11347.574| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.85 r_work: 0.2833 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10365 Z= 0.117 Angle : 0.493 8.526 14127 Z= 0.249 Chirality : 0.045 0.138 1773 Planarity : 0.003 0.037 1749 Dihedral : 4.962 53.979 1645 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.99 % Allowed : 15.67 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.23), residues: 1302 helix: 1.96 (0.26), residues: 447 sheet: 0.29 (0.31), residues: 258 loop : -0.09 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 244 TYR 0.017 0.001 TYR B 248 PHE 0.008 0.001 PHE B 301 TRP 0.002 0.001 TRP A 308 HIS 0.002 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00285 (10335) covalent geometry : angle 0.48052 (14055) SS BOND : bond 0.00172 ( 18) SS BOND : angle 1.59273 ( 36) hydrogen bonds : bond 0.02884 ( 409) hydrogen bonds : angle 4.27788 ( 1164) link_NAG-ASN : bond 0.00152 ( 12) link_NAG-ASN : angle 1.68295 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2995.33 seconds wall clock time: 52 minutes 6.75 seconds (3126.75 seconds total)