Starting phenix.real_space_refine on Fri Feb 14 14:05:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnr_27577/02_2025/8dnr_27577_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnr_27577/02_2025/8dnr_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_27577/02_2025/8dnr_27577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnr_27577/02_2025/8dnr_27577.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnr_27577/02_2025/8dnr_27577_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnr_27577/02_2025/8dnr_27577_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.074 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLU:plan': 2, 'ARG:plan': 1, '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: {'GLU:plan': 2, 'ARG:plan': 1, '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: {'GLU:plan': 2, 'ARG:plan': 1, '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: 6.44, per 1000 atoms: 0.63 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: 2.43 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.48 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: 3.92 Time building geometry restraints manager: 2.84 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: 0.03 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.530 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 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:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.810 ------------------------------------------------------------------------------- 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 10335 Z= 0.217 Angle : 0.521 8.218 14055 Z= 0.289 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 : 5.07 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (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 TRP 0.002 0.000 TRP A 308 HIS 0.004 0.001 HIS E 102 PHE 0.007 0.001 PHE B 301 TYR 0.009 0.001 TYR E 432 ARG 0.002 0.000 ARG B 244 *********************** 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 : 1.192 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: 0.7513 (m) cc_final: 0.6775 (t) outliers start: 17 outliers final: 13 residues processed: 131 average time/residue: 0.9533 time to fit residues: 137.6445 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 : 1.199 ------------------------------------------------------------------------------- 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 108 optimal weight: 3.9990 chunk 97 optimal weight: 0.0770 chunk 54 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 0.0570 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 314 ASN E 102 HIS E 194 GLN E 314 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.091647 restraints weight = 11820.207| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.87 r_work: 0.2809 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10335 Z= 0.142 Angle : 0.449 4.798 14055 Z= 0.239 Chirality : 0.044 0.152 1773 Planarity : 0.003 0.036 1749 Dihedral : 7.129 60.440 1667 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.68 % Allowed : 13.33 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.23), residues: 1302 helix: 1.84 (0.26), residues: 429 sheet: 0.27 (0.31), residues: 258 loop : -0.39 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 308 HIS 0.001 0.000 HIS B 102 PHE 0.007 0.001 PHE B 301 TYR 0.016 0.001 TYR B 248 ARG 0.002 0.000 ARG A 375 *********************** 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 153 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 1.027 Fit side-chains REVERT: A 95 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7719 (mm-30) REVERT: A 335 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8708 (mptp) REVERT: B 220 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: E 74 THR cc_start: 0.8187 (m) cc_final: 0.7985 (m) REVERT: E 250 THR cc_start: 0.7432 (m) cc_final: 0.6644 (t) outliers start: 31 outliers final: 9 residues processed: 139 average time/residue: 0.9015 time to fit residues: 139.1438 Evaluate side-chains 119 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.179 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 100 optimal weight: 0.9980 chunk 50 optimal weight: 0.1980 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 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 = 0.3269 r_free = 0.3269 target = 0.116615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.094014 restraints weight = 11476.479| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.86 r_work: 0.2843 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10335 Z= 0.178 Angle : 0.455 4.781 14055 Z= 0.239 Chirality : 0.045 0.148 1773 Planarity : 0.003 0.036 1749 Dihedral : 6.184 54.597 1647 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.29 % Allowed : 13.07 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.23), residues: 1302 helix: 1.94 (0.26), residues: 429 sheet: 0.27 (0.31), residues: 258 loop : -0.35 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 308 HIS 0.001 0.001 HIS B 29 PHE 0.008 0.001 PHE B 301 TYR 0.009 0.001 TYR B 275 ARG 0.003 0.000 ARG B 244 *********************** 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 147 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 109 time to evaluate : 1.100 Fit side-chains REVERT: A 95 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7695 (mt-10) REVERT: A 335 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8703 (mptp) REVERT: B 220 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.7987 (m-30) outliers start: 38 outliers final: 13 residues processed: 130 average time/residue: 0.9140 time to fit residues: 131.2066 Evaluate side-chains 119 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 B residue 103 ASP 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 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 422 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 58 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 80 optimal weight: 0.0670 chunk 83 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.9724 ------------------------------------------------------------------------------- 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 = 0.3201 r_free = 0.3201 target = 0.111665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.089139 restraints weight = 11391.706| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.83 r_work: 0.2791 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10335 Z= 0.383 Angle : 0.559 6.025 14055 Z= 0.289 Chirality : 0.049 0.149 1773 Planarity : 0.004 0.040 1749 Dihedral : 6.475 57.358 1647 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.22), residues: 1302 helix: 1.41 (0.25), residues: 441 sheet: 0.22 (0.31), residues: 258 loop : -0.40 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 308 HIS 0.003 0.001 HIS B 29 PHE 0.013 0.002 PHE B 301 TYR 0.018 0.002 TYR B 275 ARG 0.003 0.000 ARG B 244 *********************** 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 145 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 103 time to evaluate : 1.091 Fit side-chains REVERT: A 335 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8624 (mptp) REVERT: E 74 THR cc_start: 0.8439 (m) cc_final: 0.8233 (m) REVERT: E 355 CYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8336 (t) outliers start: 42 outliers final: 16 residues processed: 126 average time/residue: 0.9575 time to fit residues: 133.0099 Evaluate side-chains 117 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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 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 355 CYS Chi-restraints excluded: chain E residue 415 THR 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 109 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3212 r_free = 0.3212 target = 0.112475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.089956 restraints weight = 11519.888| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.85 r_work: 0.2779 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10335 Z= 0.268 Angle : 0.500 4.704 14055 Z= 0.261 Chirality : 0.047 0.146 1773 Planarity : 0.003 0.039 1749 Dihedral : 6.156 57.129 1647 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.81 % Allowed : 12.64 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1302 helix: 1.48 (0.25), residues: 441 sheet: 0.17 (0.31), residues: 258 loop : -0.34 (0.23), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 308 HIS 0.002 0.001 HIS B 29 PHE 0.011 0.001 PHE B 301 TYR 0.012 0.001 TYR B 275 ARG 0.002 0.000 ARG B 244 *********************** 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 145 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 1.204 Fit side-chains REVERT: A 95 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7806 (mm-30) REVERT: A 335 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8631 (mptp) REVERT: E 74 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8173 (m) REVERT: E 96 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8226 (tm) outliers start: 44 outliers final: 15 residues processed: 126 average time/residue: 0.9534 time to fit residues: 132.5103 Evaluate side-chains 116 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 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 258 GLU Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain E residue 74 THR 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 436 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 28 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 40 optimal weight: 0.0020 chunk 38 optimal weight: 0.6980 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 = 0.3278 r_free = 0.3278 target = 0.116953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.094909 restraints weight = 11412.050| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.82 r_work: 0.2824 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 0.022 10335 Z= 0.161 Angle : 0.452 5.551 14055 Z= 0.238 Chirality : 0.045 0.146 1773 Planarity : 0.003 0.038 1749 Dihedral : 5.573 54.537 1647 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.29 % Allowed : 13.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.23), residues: 1302 helix: 1.74 (0.25), residues: 447 sheet: 0.21 (0.31), residues: 258 loop : -0.18 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 308 HIS 0.001 0.000 HIS E 372 PHE 0.008 0.001 PHE E 376 TYR 0.008 0.001 TYR A 438 ARG 0.003 0.000 ARG E 375 *********************** 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 142 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 104 time to evaluate : 1.233 Fit side-chains REVERT: A 335 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8630 (mptp) REVERT: A 422 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7928 (mt) REVERT: B 103 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6741 (m-30) REVERT: B 220 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.7949 (m-30) REVERT: E 96 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8209 (tm) outliers start: 38 outliers final: 13 residues processed: 126 average time/residue: 0.9313 time to fit residues: 130.2081 Evaluate side-chains 120 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 210 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 B residue 103 ASP 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 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 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 64 optimal weight: 0.2980 chunk 52 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 121 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 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 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 = 0.3257 r_free = 0.3257 target = 0.115764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.093009 restraints weight = 11570.733| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.87 r_work: 0.2813 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10335 Z= 0.172 Angle : 0.468 5.957 14055 Z= 0.243 Chirality : 0.045 0.141 1773 Planarity : 0.003 0.037 1749 Dihedral : 5.156 53.646 1644 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.60 % Allowed : 14.46 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.23), residues: 1302 helix: 1.83 (0.25), residues: 447 sheet: 0.22 (0.31), residues: 258 loop : -0.16 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 308 HIS 0.002 0.001 HIS A 102 PHE 0.008 0.001 PHE B 301 TYR 0.008 0.001 TYR B 248 ARG 0.002 0.000 ARG B 244 *********************** 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 133 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 1.266 Fit side-chains REVERT: A 335 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8598 (mptp) REVERT: A 422 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7943 (mt) REVERT: B 210 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8034 (tt) REVERT: B 220 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.7983 (m-30) REVERT: E 96 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8225 (tm) outliers start: 30 outliers final: 12 residues processed: 119 average time/residue: 0.9177 time to fit residues: 120.8913 Evaluate side-chains 117 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 1.369 ------------------------------------------------------------------------------- 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 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 312 VAL Chi-restraints excluded: chain E residue 422 LEU 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 44 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.3246 r_free = 0.3246 target = 0.114643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.092130 restraints weight = 11381.428| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.84 r_work: 0.2799 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10335 Z= 0.273 Angle : 0.511 6.110 14055 Z= 0.264 Chirality : 0.046 0.144 1773 Planarity : 0.003 0.038 1749 Dihedral : 5.345 54.424 1644 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.60 % Allowed : 14.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1302 helix: 1.65 (0.25), residues: 447 sheet: 0.19 (0.31), residues: 258 loop : -0.21 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 308 HIS 0.002 0.001 HIS A 102 PHE 0.011 0.001 PHE B 301 TYR 0.013 0.002 TYR B 275 ARG 0.003 0.000 ARG A 375 *********************** 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 129 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 1.220 Fit side-chains REVERT: A 335 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8573 (mptp) REVERT: A 422 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7977 (mt) REVERT: B 210 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8096 (tt) REVERT: E 96 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8230 (tm) outliers start: 30 outliers final: 15 residues processed: 116 average time/residue: 0.9604 time to fit residues: 123.2241 Evaluate side-chains 116 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 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 312 VAL 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 0 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3249 r_free = 0.3249 target = 0.114911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.092333 restraints weight = 11388.913| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.85 r_work: 0.2796 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10335 Z= 0.251 Angle : 0.502 6.486 14055 Z= 0.260 Chirality : 0.046 0.142 1773 Planarity : 0.003 0.038 1749 Dihedral : 5.313 53.782 1644 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.16 % Allowed : 15.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.23), residues: 1302 helix: 1.64 (0.25), residues: 447 sheet: 0.18 (0.31), residues: 258 loop : -0.21 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 308 HIS 0.002 0.001 HIS A 102 PHE 0.010 0.001 PHE B 301 TYR 0.011 0.001 TYR B 275 ARG 0.002 0.000 ARG A 375 *********************** 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 126 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 1.263 Fit side-chains REVERT: A 335 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8577 (mptp) REVERT: A 422 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7982 (mt) REVERT: B 210 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8071 (tt) REVERT: E 96 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8235 (tm) outliers start: 25 outliers final: 16 residues processed: 117 average time/residue: 0.9517 time to fit residues: 122.9271 Evaluate side-chains 117 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 1.221 ------------------------------------------------------------------------------- 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 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 312 VAL 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 53 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 34 optimal weight: 0.0970 chunk 96 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 121 optimal weight: 0.0030 chunk 84 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 = 0.3280 r_free = 0.3280 target = 0.117301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.095240 restraints weight = 11391.111| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.82 r_work: 0.2846 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10335 Z= 0.144 Angle : 0.451 7.052 14055 Z= 0.235 Chirality : 0.044 0.145 1773 Planarity : 0.003 0.038 1749 Dihedral : 4.952 52.766 1644 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.99 % Allowed : 15.76 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.23), residues: 1302 helix: 1.90 (0.26), residues: 447 sheet: 0.26 (0.31), residues: 258 loop : -0.11 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP B 308 HIS 0.003 0.001 HIS A 102 PHE 0.007 0.001 PHE B 301 TYR 0.011 0.001 TYR B 248 ARG 0.002 0.000 ARG B 244 ********************** 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 129 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 1.108 Fit side-chains REVERT: A 335 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8575 (mptp) REVERT: A 422 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7962 (mt) REVERT: B 220 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: E 96 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8187 (tm) outliers start: 23 outliers final: 13 residues processed: 121 average time/residue: 0.9448 time to fit residues: 127.0880 Evaluate side-chains 121 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 B residue 88 SER Chi-restraints excluded: chain B residue 103 ASP 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 96 LEU 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 100 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 23 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3268 r_free = 0.3268 target = 0.116171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.094131 restraints weight = 11282.685| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.81 r_work: 0.2813 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10335 Z= 0.242 Angle : 0.501 6.786 14055 Z= 0.257 Chirality : 0.046 0.142 1773 Planarity : 0.003 0.037 1749 Dihedral : 5.168 54.099 1644 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.08 % Allowed : 15.84 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1302 helix: 1.75 (0.25), residues: 447 sheet: 0.24 (0.31), residues: 258 loop : -0.17 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 308 HIS 0.002 0.001 HIS A 102 PHE 0.010 0.001 PHE B 301 TYR 0.017 0.001 TYR B 248 ARG 0.002 0.000 ARG A 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5705.05 seconds wall clock time: 101 minutes 57.35 seconds (6117.35 seconds total)