Starting phenix.real_space_refine on Thu Sep 18 06:57:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fgd_50396/09_2025/9fgd_50396.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fgd_50396/09_2025/9fgd_50396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9fgd_50396/09_2025/9fgd_50396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fgd_50396/09_2025/9fgd_50396.map" model { file = "/net/cci-nas-00/data/ceres_data/9fgd_50396/09_2025/9fgd_50396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fgd_50396/09_2025/9fgd_50396.cif" } resolution = 3.3 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= 0.017 sd= 0.087 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 82 5.16 5 C 9637 2.51 5 N 2418 2.21 5 O 2740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14877 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2722 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2714 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 321} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 336, 2714 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 321} Chain breaks: 1 bond proxies already assigned to first conformer: 2773 Chain: "B" Number of atoms: 2715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2715 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "C" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2728 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 317} Chain breaks: 1 Chain: "D" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2658 Classifications: {'peptide': 329} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 314} Chain breaks: 1 Chain: "E" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2716 Classifications: {'peptide': 331} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 316} Chain breaks: 1 Chain: "F" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 937 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain breaks: 1 Chain: "a" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "d" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'D10': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.47, per 1000 atoms: 0.30 Number of scatterers: 14877 At special positions: 0 Unit cell: (98.1736, 109.896, 134.806, 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 82 16.00 O 2740 8.00 N 2418 7.00 C 9637 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS F 429 " - pdb=" SG CYS F 502 " 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 ALPHA1-2 " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN a 8 " - " MAN a 9 " ALPHA1-3 " BMA G 3 " - " MAN G 6 " " MAN G 4 " - " MAN G 5 " " BMA H 3 " - " MAN H 6 " " MAN H 4 " - " MAN H 5 " " BMA a 3 " - " MAN a 4 " " MAN a 7 " - " MAN a 10 " " BMA d 3 " - " MAN d 4 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA a 3 " - " MAN a 7 " " MAN a 7 " - " MAN a 8 " " BMA d 3 " - " MAN d 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG C 501 " - " ASN C 208 " " NAG G 1 " - " ASN B 149 " " NAG H 1 " - " ASN E 149 " " NAG a 1 " - " ASN A 111 " " NAG b 1 " - " ASN B 80 " " NAG d 1 " - " ASN D 111 " " NAG e 1 " - " ASN E 80 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 722.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3372 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 14 sheets defined 39.7% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 removed outlier: 3.873A pdb=" N THR A 16 " --> pdb=" O THR A 12 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 removed outlier: 3.971A pdb=" N LYS A 76 " --> pdb=" O GLU A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 142 through 146 removed outlier: 4.557A pdb=" N ASP A 145 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 223 through 230 removed outlier: 3.568A pdb=" N ILE A 228 " --> pdb=" O GLY A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 251 through 277 removed outlier: 3.508A pdb=" N VAL A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 309 Processing helix chain 'A' and resid 390 through 416 removed outlier: 3.727A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Proline residue: A 401 - end of helix removed outlier: 3.538A pdb=" N LEU A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 21 Processing helix chain 'B' and resid 70 through 73 Processing helix chain 'B' and resid 84 through 91 removed outlier: 3.553A pdb=" N ALA B 88 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 173 Processing helix chain 'B' and resid 218 through 225 removed outlier: 3.500A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 237 removed outlier: 3.623A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 246 through 272 Processing helix chain 'B' and resid 279 through 309 removed outlier: 3.872A pdb=" N TYR B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 447 removed outlier: 3.712A pdb=" N ILE B 423 " --> pdb=" O ASP B 419 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B 424 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE B 429 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.752A pdb=" N LYS C 105 " --> pdb=" O MET C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 158 removed outlier: 4.551A pdb=" N ASN C 157 " --> pdb=" O GLN C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 196 Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.666A pdb=" N ILE C 238 " --> pdb=" O GLY C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 252 removed outlier: 3.578A pdb=" N TRP C 252 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 4.037A pdb=" N TRP C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 284 removed outlier: 3.509A pdb=" N THR C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL C 273 " --> pdb=" O GLY C 269 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 323 removed outlier: 3.563A pdb=" N LEU C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE C 320 " --> pdb=" O THR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 434 removed outlier: 3.673A pdb=" N ASP C 411 " --> pdb=" O ILE C 407 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG C 415 " --> pdb=" O ASP C 411 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.527A pdb=" N VAL C 431 " --> pdb=" O LEU C 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 24 removed outlier: 3.512A pdb=" N LEU D 22 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP D 24 " --> pdb=" O ASP D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 76 removed outlier: 3.527A pdb=" N LYS D 76 " --> pdb=" O GLU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.371A pdb=" N ASP D 145 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 223 through 230 removed outlier: 3.790A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.927A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 247 No H-bonds generated for 'chain 'D' and resid 245 through 247' Processing helix chain 'D' and resid 251 through 277 removed outlier: 3.510A pdb=" N ARG D 274 " --> pdb=" O SER D 270 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 310 removed outlier: 3.502A pdb=" N TRP D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 417 removed outlier: 4.175A pdb=" N ILE D 398 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 400 " --> pdb=" O SER D 396 " (cutoff:3.500A) Proline residue: D 401 - end of helix removed outlier: 4.008A pdb=" N ALA D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 21 Processing helix chain 'E' and resid 70 through 73 removed outlier: 3.865A pdb=" N ALA E 73 " --> pdb=" O LYS E 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 73' Processing helix chain 'E' and resid 84 through 91 removed outlier: 3.547A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 174 Processing helix chain 'E' and resid 218 through 225 removed outlier: 3.760A pdb=" N LEU E 223 " --> pdb=" O GLY E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 237 Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 246 through 272 Processing helix chain 'E' and resid 279 through 308 removed outlier: 3.603A pdb=" N MET E 283 " --> pdb=" O LYS E 279 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE E 291 " --> pdb=" O GLY E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 447 removed outlier: 4.050A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing helix chain 'F' and resid 493 through 497 Processing helix chain 'F' and resid 513 through 517 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 54 removed outlier: 6.070A pdb=" N GLU A 40 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS A 71 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ASP A 63 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N PHE A 50 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A 61 " --> pdb=" O PHE A 50 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLU A 59 " --> pdb=" O PRO A 52 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 59 through 71 current: chain 'A' and resid 126 through 138 Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.151A pdb=" N GLY A 195 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LYS A 220 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEU A 193 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 51 removed outlier: 6.590A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N MET B 49 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ASP B 56 " --> pdb=" O MET B 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 61 current: chain 'B' and resid 123 through 128 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 96 through 98 current: chain 'B' and resid 204 through 215 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 51 through 59 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 59 current: chain 'C' and resid 71 through 82 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 82 current: chain 'C' and resid 139 through 150 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 111 through 113 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 111 through 113 current: chain 'C' and resid 219 through 231 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 39 through 47 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 39 through 47 current: chain 'D' and resid 59 through 69 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 69 current: chain 'D' and resid 127 through 138 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 100 through 101 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 100 through 101 current: chain 'D' and resid 209 through 220 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 81 through 83 removed outlier: 4.338A pdb=" N ILE E 116 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU E 165 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 44 through 51 removed outlier: 6.661A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N MET E 49 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASP E 56 " --> pdb=" O MET E 49 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS E 103 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA E 135 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP E 101 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.994A pdb=" N SER E 156 " --> pdb=" O PRO E 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.680A pdb=" N SER F 432 " --> pdb=" O GLN F 4 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 12 through 13 Processing sheet with id=AB5, first strand: chain 'F' and resid 440 through 446 removed outlier: 7.008A pdb=" N MET F 441 " --> pdb=" O ALA F 457 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ALA F 457 " --> pdb=" O MET F 441 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TRP F 443 " --> pdb=" O LEU F 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 464 through 466 current: chain 'F' and resid 519 through 520 525 hydrogen bonds defined for protein. 1463 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: 2.35 Time building geometry restraints manager: 1.53 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: 4530 1.34 - 1.46: 3244 1.46 - 1.57: 7335 1.57 - 1.69: 0 1.69 - 1.81: 141 Bond restraints: 15250 Sorted by residual: bond pdb=" C1 MAN a 9 " pdb=" O5 MAN a 9 " ideal model delta sigma weight residual 1.399 1.438 -0.039 2.00e-02 2.50e+03 3.71e+00 bond pdb=" C1 MAN a 8 " pdb=" O5 MAN a 8 " ideal model delta sigma weight residual 1.399 1.437 -0.038 2.00e-02 2.50e+03 3.58e+00 bond pdb=" C1 MAN a 10 " pdb=" O5 MAN a 10 " ideal model delta sigma weight residual 1.399 1.436 -0.037 2.00e-02 2.50e+03 3.42e+00 bond pdb=" C1 MAN a 4 " pdb=" O5 MAN a 4 " ideal model delta sigma weight residual 1.399 1.435 -0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C1 MAN H 4 " pdb=" O5 MAN H 4 " ideal model delta sigma weight residual 1.399 1.432 -0.033 2.00e-02 2.50e+03 2.78e+00 ... (remaining 15245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 20058 1.27 - 2.55: 490 2.55 - 3.82: 147 3.82 - 5.09: 21 5.09 - 6.37: 12 Bond angle restraints: 20728 Sorted by residual: angle pdb=" C LEU B 99 " pdb=" N ASN B 100 " pdb=" CA ASN B 100 " ideal model delta sigma weight residual 123.25 119.40 3.85 1.69e+00 3.50e-01 5.18e+00 angle pdb=" N ALA A 281 " pdb=" CA ALA A 281 " pdb=" C ALA A 281 " ideal model delta sigma weight residual 114.04 111.35 2.69 1.24e+00 6.50e-01 4.70e+00 angle pdb=" C1 MAN a 5 " pdb=" C2 MAN a 5 " pdb=" O2 MAN a 5 " ideal model delta sigma weight residual 106.80 113.17 -6.37 3.00e+00 1.11e-01 4.50e+00 angle pdb=" C1 BMA a 3 " pdb=" O5 BMA a 3 " pdb=" C5 BMA a 3 " ideal model delta sigma weight residual 118.82 112.91 5.91 3.00e+00 1.11e-01 3.89e+00 angle pdb=" C1 BMA d 3 " pdb=" O5 BMA d 3 " pdb=" C5 BMA d 3 " ideal model delta sigma weight residual 118.82 113.27 5.55 3.00e+00 1.11e-01 3.42e+00 ... (remaining 20723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 9062 21.48 - 42.97: 219 42.97 - 64.45: 26 64.45 - 85.93: 24 85.93 - 107.42: 16 Dihedral angle restraints: 9347 sinusoidal: 4104 harmonic: 5243 Sorted by residual: dihedral pdb=" CA PRO E 276 " pdb=" C PRO E 276 " pdb=" N TYR E 277 " pdb=" CA TYR E 277 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" O4 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C5 BMA a 3 " pdb=" O5 BMA a 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.71 107.42 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C3 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C5 BMA a 3 " pdb=" O5 BMA a 3 " ideal model delta sinusoidal sigma weight residual 47.62 -57.69 105.31 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 9344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.942: 2436 0.942 - 1.883: 0 1.883 - 2.825: 0 2.825 - 3.766: 0 3.766 - 4.707: 2 Chirality restraints: 2438 Sorted by residual: chirality pdb=" C1 MAN a 6 " pdb=" O2 MAN a 5 " pdb=" C2 MAN a 6 " pdb=" O5 MAN a 6 " both_signs ideal model delta sigma weight residual False 2.40 -2.31 4.71 2.00e-02 2.50e+03 5.54e+04 chirality pdb=" C1 MAN a 5 " pdb=" O2 MAN a 4 " pdb=" C2 MAN a 5 " pdb=" O5 MAN a 5 " both_signs ideal model delta sigma weight residual False 2.40 -2.22 4.62 2.00e-02 2.50e+03 5.34e+04 chirality pdb=" C2 MAN a 5 " pdb=" C1 MAN a 5 " pdb=" C3 MAN a 5 " pdb=" O2 MAN a 5 " both_signs ideal model delta sigma weight residual False 2.52 2.12 0.39 2.00e-01 2.50e+01 3.85e+00 ... (remaining 2435 not shown) Planarity restraints: 2527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 275 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.83e+00 pdb=" N PRO E 276 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 276 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 276 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 275 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO B 276 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 146 " -0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO A 147 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 147 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 147 " -0.017 5.00e-02 4.00e+02 ... (remaining 2524 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3558 2.79 - 3.32: 13905 3.32 - 3.84: 24345 3.84 - 4.37: 29175 4.37 - 4.90: 50360 Nonbonded interactions: 121343 Sorted by model distance: nonbonded pdb=" ND2 ASN C 66 " pdb=" OD1 ASN C 69 " model vdw 2.259 3.120 nonbonded pdb=" OG1 THR D 99 " pdb=" OH TYR D 169 " model vdw 2.260 3.040 nonbonded pdb=" O TYR C 199 " pdb=" NH2 ARG C 232 " model vdw 2.261 3.120 nonbonded pdb=" OG1 THR C 111 " pdb=" OH TYR C 181 " model vdw 2.266 3.040 nonbonded pdb=" OE1 GLN F 464 " pdb=" OH TYR F 466 " model vdw 2.273 3.040 ... (remaining 121338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 66 or resid 68 through 311 or resid 388 through \ 417)) selection = (chain 'D' and (resid 13 through 66 or resid 68 through 417)) } ncs_group { reference = (chain 'B' and (resid 10 through 310 or resid 420 through 447)) selection = (chain 'E' and resid 10 through 447) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = 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=0.50 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: 0.590 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: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.860 Find NCS groups from input model: 0.270 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 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 : 0.005 0.039 15288 Z= 0.231 Angle : 0.553 9.811 20836 Z= 0.257 Chirality : 0.140 4.707 2438 Planarity : 0.003 0.034 2520 Dihedral : 11.581 107.418 5957 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.07 % Allowed : 4.09 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.58 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: 0.31 (0.21), residues: 1755 helix: 1.57 (0.22), residues: 537 sheet: -0.68 (0.25), residues: 488 loop : -0.02 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 265 TYR 0.012 0.001 TYR B 277 PHE 0.012 0.001 PHE D 146 TRP 0.007 0.001 TRP B 67 HIS 0.004 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00515 (15250) covalent geometry : angle 0.53915 (20728) SS BOND : bond 0.00097 ( 6) SS BOND : angle 0.65118 ( 12) hydrogen bonds : bond 0.26446 ( 525) hydrogen bonds : angle 7.77250 ( 1463) link_ALPHA1-2 : bond 0.01165 ( 3) link_ALPHA1-2 : angle 3.61393 ( 9) link_ALPHA1-3 : bond 0.00616 ( 7) link_ALPHA1-3 : angle 1.50603 ( 21) link_ALPHA1-6 : bond 0.00760 ( 5) link_ALPHA1-6 : angle 1.90357 ( 15) link_BETA1-4 : bond 0.00445 ( 10) link_BETA1-4 : angle 1.57194 ( 30) link_NAG-ASN : bond 0.00259 ( 7) link_NAG-ASN : angle 1.45290 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.9300 (mtp) cc_final: 0.8980 (mtp) REVERT: A 81 MET cc_start: 0.8775 (pmm) cc_final: 0.8500 (pmm) REVERT: A 229 GLN cc_start: 0.9228 (mm110) cc_final: 0.8932 (mm-40) REVERT: A 293 CYS cc_start: 0.9095 (m) cc_final: 0.8597 (m) REVERT: B 41 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.8843 (t0) REVERT: B 49 MET cc_start: 0.8942 (mmm) cc_final: 0.8545 (tpp) REVERT: B 155 GLU cc_start: 0.8448 (tt0) cc_final: 0.8241 (tt0) REVERT: B 270 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8866 (mm-30) REVERT: C 70 MET cc_start: 0.9469 (mmt) cc_final: 0.8499 (mmm) REVERT: C 196 TRP cc_start: 0.8405 (m-10) cc_final: 0.7978 (m-10) REVERT: D 114 MET cc_start: 0.9210 (mmm) cc_final: 0.9010 (mmm) REVERT: D 258 PHE cc_start: 0.8768 (t80) cc_final: 0.8566 (t80) REVERT: D 288 TRP cc_start: 0.7639 (m100) cc_final: 0.7196 (m-10) REVERT: E 9 MET cc_start: 0.8531 (ttt) cc_final: 0.8033 (ttt) REVERT: E 13 LYS cc_start: 0.9596 (tttm) cc_final: 0.9307 (ttpt) REVERT: E 90 GLN cc_start: 0.9262 (mt0) cc_final: 0.8746 (mp10) REVERT: E 153 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8464 (mm-30) REVERT: F 435 THR cc_start: 0.8725 (m) cc_final: 0.8313 (t) REVERT: F 445 ARG cc_start: 0.8673 (ttp-170) cc_final: 0.8109 (tmm-80) REVERT: F 458 MET cc_start: 0.7217 (ttm) cc_final: 0.6638 (ttm) REVERT: F 488 GLN cc_start: 0.8576 (tp40) cc_final: 0.8099 (tm-30) REVERT: F 517 TYR cc_start: 0.7575 (m-80) cc_final: 0.7016 (m-80) REVERT: F 520 TRP cc_start: 0.8134 (m100) cc_final: 0.7175 (m100) outliers start: 17 outliers final: 8 residues processed: 204 average time/residue: 0.1436 time to fit residues: 41.8004 Evaluate side-chains 146 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 387 ASN B 41 ASN B 65 GLN B 303 ASN C 66 ASN C 69 ASN C 122 HIS C 128 ASN C 323 ASN D 110 HIS D 229 GLN D 248 ASN E 243 ASN ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.070470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.051918 restraints weight = 89860.842| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 4.95 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15288 Z= 0.130 Angle : 0.569 7.756 20836 Z= 0.288 Chirality : 0.042 0.170 2438 Planarity : 0.004 0.040 2520 Dihedral : 10.282 91.242 2645 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.32 % Allowed : 7.12 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.58 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: 0.90 (0.21), residues: 1755 helix: 2.16 (0.21), residues: 570 sheet: -0.51 (0.25), residues: 457 loop : 0.23 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 269 TYR 0.019 0.001 TYR E 299 PHE 0.016 0.001 PHE A 304 TRP 0.010 0.001 TRP E 426 HIS 0.009 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00274 (15250) covalent geometry : angle 0.55807 (20728) SS BOND : bond 0.00104 ( 6) SS BOND : angle 0.57843 ( 12) hydrogen bonds : bond 0.05781 ( 525) hydrogen bonds : angle 5.05938 ( 1463) link_ALPHA1-2 : bond 0.00647 ( 3) link_ALPHA1-2 : angle 2.07243 ( 9) link_ALPHA1-3 : bond 0.00885 ( 7) link_ALPHA1-3 : angle 1.73408 ( 21) link_ALPHA1-6 : bond 0.00513 ( 5) link_ALPHA1-6 : angle 2.14898 ( 15) link_BETA1-4 : bond 0.00300 ( 10) link_BETA1-4 : angle 1.59593 ( 30) link_NAG-ASN : bond 0.00321 ( 7) link_NAG-ASN : angle 1.38047 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.9103 (mtp) cc_final: 0.8568 (mtp) REVERT: A 81 MET cc_start: 0.8766 (pmm) cc_final: 0.8471 (pmm) REVERT: A 141 MET cc_start: 0.8945 (mtt) cc_final: 0.8631 (mtt) REVERT: A 266 MET cc_start: 0.9224 (mmm) cc_final: 0.8943 (tpt) REVERT: A 293 CYS cc_start: 0.9001 (m) cc_final: 0.8516 (m) REVERT: B 61 MET cc_start: 0.9174 (ptp) cc_final: 0.8909 (ptp) REVERT: B 182 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8461 (mm-30) REVERT: B 270 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8619 (mm-30) REVERT: B 298 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8877 (tm-30) REVERT: C 70 MET cc_start: 0.9198 (mmt) cc_final: 0.8810 (mmm) REVERT: C 71 GLU cc_start: 0.9068 (pt0) cc_final: 0.8358 (pm20) REVERT: C 189 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7152 (mm-30) REVERT: D 114 MET cc_start: 0.8992 (mmm) cc_final: 0.8704 (mmm) REVERT: D 258 PHE cc_start: 0.8789 (t80) cc_final: 0.8530 (t80) REVERT: D 288 TRP cc_start: 0.7286 (m100) cc_final: 0.6743 (m-10) REVERT: E 9 MET cc_start: 0.8472 (ttt) cc_final: 0.7782 (ttt) REVERT: E 55 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8569 (mtp) REVERT: E 90 GLN cc_start: 0.9459 (mt0) cc_final: 0.8674 (mp10) REVERT: E 153 GLU cc_start: 0.8753 (mm-30) cc_final: 0.7833 (mm-30) REVERT: E 237 TRP cc_start: 0.9073 (m-10) cc_final: 0.8607 (m-10) REVERT: E 267 HIS cc_start: 0.8474 (m-70) cc_final: 0.7805 (m-70) REVERT: F 435 THR cc_start: 0.7613 (m) cc_final: 0.7269 (t) REVERT: F 441 MET cc_start: 0.7703 (mtp) cc_final: 0.7442 (mtp) REVERT: F 445 ARG cc_start: 0.8196 (ttp-170) cc_final: 0.7683 (tmm-80) REVERT: F 458 MET cc_start: 0.5524 (ttm) cc_final: 0.4604 (ttm) REVERT: F 462 ARG cc_start: 0.8279 (mtp85) cc_final: 0.7906 (mpp80) REVERT: F 475 THR cc_start: 0.8486 (m) cc_final: 0.8022 (p) REVERT: F 479 ASP cc_start: 0.7885 (t0) cc_final: 0.7394 (t0) REVERT: F 482 LYS cc_start: 0.9411 (mtpp) cc_final: 0.8931 (mtmm) REVERT: F 488 GLN cc_start: 0.8176 (tp40) cc_final: 0.7568 (tm-30) REVERT: F 517 TYR cc_start: 0.8114 (m-80) cc_final: 0.7384 (m-80) REVERT: F 520 TRP cc_start: 0.7801 (m100) cc_final: 0.7302 (m100) outliers start: 21 outliers final: 9 residues processed: 170 average time/residue: 0.1299 time to fit residues: 33.1772 Evaluate side-chains 146 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 52 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.069674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.050872 restraints weight = 99192.072| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 5.17 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15288 Z= 0.187 Angle : 0.567 9.434 20836 Z= 0.280 Chirality : 0.042 0.180 2438 Planarity : 0.003 0.045 2520 Dihedral : 9.091 73.755 2638 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.26 % Allowed : 7.49 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.58 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: 0.91 (0.21), residues: 1755 helix: 2.22 (0.21), residues: 572 sheet: -0.62 (0.25), residues: 464 loop : 0.28 (0.25), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.023 0.001 TYR E 299 PHE 0.019 0.001 PHE F 454 TRP 0.017 0.001 TRP C 196 HIS 0.003 0.001 HIS E 267 Details of bonding type rmsd covalent geometry : bond 0.00414 (15250) covalent geometry : angle 0.55562 (20728) SS BOND : bond 0.00113 ( 6) SS BOND : angle 0.54899 ( 12) hydrogen bonds : bond 0.04826 ( 525) hydrogen bonds : angle 4.73589 ( 1463) link_ALPHA1-2 : bond 0.01068 ( 3) link_ALPHA1-2 : angle 2.19758 ( 9) link_ALPHA1-3 : bond 0.00884 ( 7) link_ALPHA1-3 : angle 1.83965 ( 21) link_ALPHA1-6 : bond 0.00510 ( 5) link_ALPHA1-6 : angle 2.09314 ( 15) link_BETA1-4 : bond 0.00345 ( 10) link_BETA1-4 : angle 1.47665 ( 30) link_NAG-ASN : bond 0.00276 ( 7) link_NAG-ASN : angle 1.36727 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.9139 (mtp) cc_final: 0.8470 (mtp) REVERT: A 81 MET cc_start: 0.8741 (pmm) cc_final: 0.8474 (pmm) REVERT: A 141 MET cc_start: 0.9011 (mtt) cc_final: 0.8504 (mtt) REVERT: A 229 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8715 (mm-40) REVERT: A 266 MET cc_start: 0.9176 (mmm) cc_final: 0.8909 (tpt) REVERT: A 293 CYS cc_start: 0.9065 (m) cc_final: 0.8571 (m) REVERT: B 182 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8412 (mm-30) REVERT: B 270 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8669 (mm-30) REVERT: B 298 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8875 (tm-30) REVERT: C 70 MET cc_start: 0.9379 (mmt) cc_final: 0.8786 (mmm) REVERT: C 71 GLU cc_start: 0.9097 (pt0) cc_final: 0.8401 (pm20) REVERT: C 189 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7166 (mm-30) REVERT: C 239 GLN cc_start: 0.8655 (mm110) cc_final: 0.8217 (tt0) REVERT: D 114 MET cc_start: 0.8960 (mmm) cc_final: 0.8658 (mmm) REVERT: D 258 PHE cc_start: 0.8864 (t80) cc_final: 0.8618 (t80) REVERT: D 288 TRP cc_start: 0.7358 (m100) cc_final: 0.6827 (m-10) REVERT: E 9 MET cc_start: 0.8371 (ttt) cc_final: 0.7727 (ttt) REVERT: E 55 MET cc_start: 0.9320 (mtp) cc_final: 0.8600 (mtp) REVERT: E 90 GLN cc_start: 0.9427 (mt0) cc_final: 0.8717 (mp10) REVERT: E 115 MET cc_start: 0.8474 (ptp) cc_final: 0.8191 (ptm) REVERT: E 237 TRP cc_start: 0.9121 (m-10) cc_final: 0.8656 (m-10) REVERT: E 267 HIS cc_start: 0.8494 (m-70) cc_final: 0.7898 (m-70) REVERT: E 269 ARG cc_start: 0.8629 (tpp-160) cc_final: 0.8415 (tpp-160) REVERT: E 286 MET cc_start: 0.8945 (tpt) cc_final: 0.8724 (tpt) REVERT: F 435 THR cc_start: 0.7806 (m) cc_final: 0.7405 (t) REVERT: F 441 MET cc_start: 0.7726 (mtp) cc_final: 0.7510 (mtp) REVERT: F 445 ARG cc_start: 0.8204 (ttp-170) cc_final: 0.7905 (tmm-80) REVERT: F 458 MET cc_start: 0.5747 (ttm) cc_final: 0.5169 (ttp) REVERT: F 462 ARG cc_start: 0.8436 (mtp85) cc_final: 0.8002 (mpp80) REVERT: F 475 THR cc_start: 0.8381 (m) cc_final: 0.7937 (p) REVERT: F 479 ASP cc_start: 0.7842 (t0) cc_final: 0.7373 (t0) REVERT: F 482 LYS cc_start: 0.9458 (mtpp) cc_final: 0.9075 (mtmm) REVERT: F 488 GLN cc_start: 0.8114 (tp40) cc_final: 0.7576 (tm-30) REVERT: F 520 TRP cc_start: 0.7818 (m100) cc_final: 0.7334 (m100) outliers start: 20 outliers final: 15 residues processed: 154 average time/residue: 0.1340 time to fit residues: 31.0918 Evaluate side-chains 144 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 17 optimal weight: 0.0060 chunk 147 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 169 optimal weight: 9.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.068508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.051213 restraints weight = 65847.742| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 4.29 r_work: 0.2730 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15288 Z= 0.106 Angle : 0.524 9.641 20836 Z= 0.258 Chirality : 0.041 0.206 2438 Planarity : 0.003 0.045 2520 Dihedral : 7.970 64.773 2637 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.20 % Allowed : 8.00 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.58 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: 0.98 (0.21), residues: 1755 helix: 2.22 (0.21), residues: 570 sheet: -0.50 (0.25), residues: 457 loop : 0.32 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 85 TYR 0.022 0.001 TYR E 299 PHE 0.021 0.001 PHE E 221 TRP 0.014 0.001 TRP E 426 HIS 0.007 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00221 (15250) covalent geometry : angle 0.51381 (20728) SS BOND : bond 0.00074 ( 6) SS BOND : angle 0.52636 ( 12) hydrogen bonds : bond 0.04044 ( 525) hydrogen bonds : angle 4.49058 ( 1463) link_ALPHA1-2 : bond 0.01304 ( 3) link_ALPHA1-2 : angle 2.14525 ( 9) link_ALPHA1-3 : bond 0.00983 ( 7) link_ALPHA1-3 : angle 1.80894 ( 21) link_ALPHA1-6 : bond 0.00644 ( 5) link_ALPHA1-6 : angle 1.77098 ( 15) link_BETA1-4 : bond 0.00344 ( 10) link_BETA1-4 : angle 1.35783 ( 30) link_NAG-ASN : bond 0.00168 ( 7) link_NAG-ASN : angle 1.19816 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.9344 (mtp) cc_final: 0.9040 (mtp) REVERT: A 81 MET cc_start: 0.8741 (pmm) cc_final: 0.8494 (pmm) REVERT: A 122 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8237 (p) REVERT: A 141 MET cc_start: 0.9026 (mtt) cc_final: 0.8785 (mtt) REVERT: A 266 MET cc_start: 0.9616 (mmm) cc_final: 0.9365 (tpt) REVERT: A 293 CYS cc_start: 0.9266 (m) cc_final: 0.8772 (m) REVERT: B 49 MET cc_start: 0.8672 (tpt) cc_final: 0.8447 (tpp) REVERT: B 155 GLU cc_start: 0.7671 (mp0) cc_final: 0.7452 (mp0) REVERT: B 182 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8846 (mm-30) REVERT: B 261 MET cc_start: 0.9585 (mmm) cc_final: 0.8836 (tpt) REVERT: B 270 GLU cc_start: 0.9374 (mt-10) cc_final: 0.8849 (mm-30) REVERT: B 298 GLU cc_start: 0.9380 (tm-30) cc_final: 0.9069 (tm-30) REVERT: C 70 MET cc_start: 0.9470 (mmt) cc_final: 0.9126 (mmm) REVERT: C 71 GLU cc_start: 0.9289 (pt0) cc_final: 0.8573 (pm20) REVERT: C 189 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7645 (mm-30) REVERT: D 114 MET cc_start: 0.9156 (mmm) cc_final: 0.8840 (mmm) REVERT: D 258 PHE cc_start: 0.8831 (t80) cc_final: 0.8493 (t80) REVERT: D 288 TRP cc_start: 0.7620 (m100) cc_final: 0.7116 (m-10) REVERT: E 9 MET cc_start: 0.8267 (ttt) cc_final: 0.7648 (ttt) REVERT: E 90 GLN cc_start: 0.9473 (mt0) cc_final: 0.8972 (mp10) REVERT: E 115 MET cc_start: 0.8887 (ptp) cc_final: 0.8542 (ptm) REVERT: E 153 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8208 (mm-30) REVERT: E 237 TRP cc_start: 0.9140 (m-10) cc_final: 0.8799 (m-10) REVERT: E 267 HIS cc_start: 0.8460 (m90) cc_final: 0.7884 (m90) REVERT: E 269 ARG cc_start: 0.8672 (tpp-160) cc_final: 0.8341 (tpp-160) REVERT: E 286 MET cc_start: 0.9326 (tpt) cc_final: 0.9053 (tpt) REVERT: F 435 THR cc_start: 0.7895 (m) cc_final: 0.7480 (t) REVERT: F 441 MET cc_start: 0.7978 (mtp) cc_final: 0.7695 (mtp) REVERT: F 445 ARG cc_start: 0.8362 (ttp-170) cc_final: 0.7793 (tmm-80) REVERT: F 446 GLN cc_start: 0.8574 (pp30) cc_final: 0.7968 (tp40) REVERT: F 458 MET cc_start: 0.5903 (ttm) cc_final: 0.5395 (ttp) REVERT: F 474 PHE cc_start: 0.8546 (m-10) cc_final: 0.8331 (m-10) REVERT: F 475 THR cc_start: 0.8445 (m) cc_final: 0.7957 (p) REVERT: F 479 ASP cc_start: 0.7828 (t0) cc_final: 0.7294 (t0) REVERT: F 482 LYS cc_start: 0.9486 (mtpp) cc_final: 0.9045 (mtmm) REVERT: F 488 GLN cc_start: 0.8215 (tp40) cc_final: 0.7557 (tm-30) REVERT: F 520 TRP cc_start: 0.8007 (m100) cc_final: 0.7324 (m100) outliers start: 19 outliers final: 12 residues processed: 157 average time/residue: 0.1263 time to fit residues: 29.9005 Evaluate side-chains 140 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 87 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 86 optimal weight: 0.0870 chunk 100 optimal weight: 4.9990 chunk 89 optimal weight: 0.2980 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.068308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.050972 restraints weight = 65300.745| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 4.29 r_work: 0.2728 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15288 Z= 0.117 Angle : 0.521 11.200 20836 Z= 0.255 Chirality : 0.041 0.212 2438 Planarity : 0.003 0.045 2520 Dihedral : 7.380 61.688 2636 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.01 % Allowed : 8.94 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.58 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: 1.03 (0.21), residues: 1755 helix: 2.24 (0.21), residues: 573 sheet: -0.50 (0.25), residues: 463 loop : 0.38 (0.25), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 85 TYR 0.022 0.001 TYR E 299 PHE 0.013 0.001 PHE E 221 TRP 0.013 0.001 TRP E 426 HIS 0.011 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00256 (15250) covalent geometry : angle 0.51060 (20728) SS BOND : bond 0.00070 ( 6) SS BOND : angle 0.45686 ( 12) hydrogen bonds : bond 0.03875 ( 525) hydrogen bonds : angle 4.37247 ( 1463) link_ALPHA1-2 : bond 0.01014 ( 3) link_ALPHA1-2 : angle 1.74727 ( 9) link_ALPHA1-3 : bond 0.00902 ( 7) link_ALPHA1-3 : angle 1.90693 ( 21) link_ALPHA1-6 : bond 0.00585 ( 5) link_ALPHA1-6 : angle 1.85859 ( 15) link_BETA1-4 : bond 0.00329 ( 10) link_BETA1-4 : angle 1.35582 ( 30) link_NAG-ASN : bond 0.00159 ( 7) link_NAG-ASN : angle 1.22604 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.9372 (mtp) cc_final: 0.8788 (mtp) REVERT: A 81 MET cc_start: 0.8738 (pmm) cc_final: 0.8508 (pmm) REVERT: A 122 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8236 (p) REVERT: A 141 MET cc_start: 0.9037 (mtt) cc_final: 0.8504 (mtt) REVERT: A 266 MET cc_start: 0.9625 (mmm) cc_final: 0.9342 (tpt) REVERT: A 293 CYS cc_start: 0.9275 (m) cc_final: 0.8789 (m) REVERT: B 49 MET cc_start: 0.8675 (tpt) cc_final: 0.8471 (tpp) REVERT: B 155 GLU cc_start: 0.7749 (mp0) cc_final: 0.7502 (mp0) REVERT: B 182 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8880 (mm-30) REVERT: B 261 MET cc_start: 0.9610 (mmm) cc_final: 0.9248 (mmm) REVERT: B 270 GLU cc_start: 0.9399 (mt-10) cc_final: 0.8814 (mm-30) REVERT: B 298 GLU cc_start: 0.9399 (tm-30) cc_final: 0.9073 (tm-30) REVERT: C 70 MET cc_start: 0.9488 (mmt) cc_final: 0.9029 (mmm) REVERT: C 71 GLU cc_start: 0.9294 (pt0) cc_final: 0.8624 (pm20) REVERT: C 189 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7681 (mm-30) REVERT: C 239 GLN cc_start: 0.8971 (mm110) cc_final: 0.8508 (mt0) REVERT: D 81 MET cc_start: 0.8319 (pmm) cc_final: 0.8036 (pmm) REVERT: D 114 MET cc_start: 0.9187 (mmm) cc_final: 0.8806 (mmm) REVERT: D 258 PHE cc_start: 0.8890 (t80) cc_final: 0.8543 (t80) REVERT: D 288 TRP cc_start: 0.7666 (m100) cc_final: 0.7171 (m-10) REVERT: E 9 MET cc_start: 0.8399 (ttt) cc_final: 0.7783 (ttt) REVERT: E 90 GLN cc_start: 0.9489 (mt0) cc_final: 0.9027 (mp10) REVERT: E 115 MET cc_start: 0.8855 (ptp) cc_final: 0.8483 (ptm) REVERT: E 153 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8182 (mm-30) REVERT: E 237 TRP cc_start: 0.9155 (m-10) cc_final: 0.8842 (m-10) REVERT: E 267 HIS cc_start: 0.8673 (m90) cc_final: 0.8153 (m90) REVERT: E 269 ARG cc_start: 0.8619 (tpp-160) cc_final: 0.8343 (tpp-160) REVERT: E 286 MET cc_start: 0.9240 (tpt) cc_final: 0.9005 (tpt) REVERT: F 435 THR cc_start: 0.7884 (m) cc_final: 0.7526 (t) REVERT: F 445 ARG cc_start: 0.8195 (ttp-170) cc_final: 0.7879 (tmm-80) REVERT: F 458 MET cc_start: 0.5783 (ttm) cc_final: 0.5235 (ttp) REVERT: F 474 PHE cc_start: 0.8546 (m-10) cc_final: 0.8310 (m-10) REVERT: F 475 THR cc_start: 0.8451 (m) cc_final: 0.7972 (p) REVERT: F 479 ASP cc_start: 0.7900 (t0) cc_final: 0.7377 (t0) REVERT: F 482 LYS cc_start: 0.9495 (mtpp) cc_final: 0.9039 (mtmm) REVERT: F 488 GLN cc_start: 0.8160 (tp40) cc_final: 0.7483 (tm-30) REVERT: F 512 ARG cc_start: 0.7635 (mtt-85) cc_final: 0.7430 (mtt90) REVERT: F 520 TRP cc_start: 0.8050 (m100) cc_final: 0.7185 (m100) outliers start: 16 outliers final: 14 residues processed: 153 average time/residue: 0.1391 time to fit residues: 31.3799 Evaluate side-chains 147 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain D residue 136 ARG Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 59 optimal weight: 0.9990 chunk 110 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 115 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.067561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.049361 restraints weight = 105931.783| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 5.35 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15288 Z= 0.176 Angle : 0.556 12.147 20836 Z= 0.272 Chirality : 0.042 0.209 2438 Planarity : 0.003 0.043 2520 Dihedral : 7.165 59.333 2636 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.13 % Allowed : 9.57 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.58 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: 1.00 (0.21), residues: 1755 helix: 2.27 (0.21), residues: 573 sheet: -0.54 (0.25), residues: 465 loop : 0.34 (0.25), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 85 TYR 0.023 0.001 TYR E 299 PHE 0.013 0.001 PHE D 304 TRP 0.012 0.001 TRP E 426 HIS 0.010 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00394 (15250) covalent geometry : angle 0.54690 (20728) SS BOND : bond 0.00098 ( 6) SS BOND : angle 0.45609 ( 12) hydrogen bonds : bond 0.03885 ( 525) hydrogen bonds : angle 4.39787 ( 1463) link_ALPHA1-2 : bond 0.00971 ( 3) link_ALPHA1-2 : angle 1.48024 ( 9) link_ALPHA1-3 : bond 0.00851 ( 7) link_ALPHA1-3 : angle 1.96617 ( 21) link_ALPHA1-6 : bond 0.00518 ( 5) link_ALPHA1-6 : angle 1.99417 ( 15) link_BETA1-4 : bond 0.00311 ( 10) link_BETA1-4 : angle 1.35174 ( 30) link_NAG-ASN : bond 0.00253 ( 7) link_NAG-ASN : angle 1.29228 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.9083 (mtp) cc_final: 0.8397 (mtp) REVERT: A 81 MET cc_start: 0.8706 (pmm) cc_final: 0.8502 (pmm) REVERT: A 141 MET cc_start: 0.8930 (mtt) cc_final: 0.8397 (mtt) REVERT: A 266 MET cc_start: 0.9231 (mmm) cc_final: 0.8903 (tpt) REVERT: A 293 CYS cc_start: 0.9090 (m) cc_final: 0.8581 (m) REVERT: B 49 MET cc_start: 0.8274 (tpt) cc_final: 0.8041 (tpp) REVERT: B 155 GLU cc_start: 0.7424 (mp0) cc_final: 0.7136 (mp0) REVERT: B 182 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8591 (mm-30) REVERT: B 261 MET cc_start: 0.9489 (mmm) cc_final: 0.9095 (mmm) REVERT: B 270 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8571 (mm-30) REVERT: B 298 GLU cc_start: 0.9246 (tm-30) cc_final: 0.8948 (tm-30) REVERT: C 70 MET cc_start: 0.9337 (mmt) cc_final: 0.8916 (mmm) REVERT: C 189 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7182 (mm-30) REVERT: C 239 GLN cc_start: 0.8677 (mm110) cc_final: 0.8349 (tt0) REVERT: D 81 MET cc_start: 0.8354 (pmm) cc_final: 0.8084 (pmm) REVERT: D 112 MET cc_start: 0.7947 (tpp) cc_final: 0.7680 (mtt) REVERT: D 114 MET cc_start: 0.8914 (mmm) cc_final: 0.8600 (mmm) REVERT: D 258 PHE cc_start: 0.8881 (t80) cc_final: 0.8566 (t80) REVERT: D 266 MET cc_start: 0.8894 (tpp) cc_final: 0.8450 (tpp) REVERT: D 288 TRP cc_start: 0.7457 (m100) cc_final: 0.6997 (m-10) REVERT: E 90 GLN cc_start: 0.9462 (mt0) cc_final: 0.8657 (mp10) REVERT: E 115 MET cc_start: 0.8489 (ptp) cc_final: 0.8177 (ptm) REVERT: E 227 MET cc_start: 0.9053 (ttp) cc_final: 0.8833 (ttp) REVERT: E 237 TRP cc_start: 0.9134 (m-10) cc_final: 0.8748 (m-10) REVERT: E 267 HIS cc_start: 0.8551 (m90) cc_final: 0.8054 (m90) REVERT: E 269 ARG cc_start: 0.8570 (tpp-160) cc_final: 0.8141 (tpp-160) REVERT: E 286 MET cc_start: 0.8907 (tpt) cc_final: 0.8649 (tpt) REVERT: F 435 THR cc_start: 0.7829 (m) cc_final: 0.7507 (t) REVERT: F 441 MET cc_start: 0.7524 (mtp) cc_final: 0.7197 (ptp) REVERT: F 445 ARG cc_start: 0.8221 (ttp-170) cc_final: 0.7828 (tmm-80) REVERT: F 458 MET cc_start: 0.5612 (ttm) cc_final: 0.4830 (ttm) REVERT: F 462 ARG cc_start: 0.8234 (mtp85) cc_final: 0.8001 (mtm180) REVERT: F 473 ARG cc_start: 0.8963 (mtm180) cc_final: 0.8029 (ptt180) REVERT: F 474 PHE cc_start: 0.8390 (m-10) cc_final: 0.8128 (m-10) REVERT: F 475 THR cc_start: 0.8504 (m) cc_final: 0.8049 (p) REVERT: F 479 ASP cc_start: 0.7949 (t0) cc_final: 0.7703 (t0) REVERT: F 488 GLN cc_start: 0.8161 (tp40) cc_final: 0.7577 (tm-30) REVERT: F 509 TRP cc_start: 0.8521 (m100) cc_final: 0.8319 (m100) REVERT: F 520 TRP cc_start: 0.8106 (m100) cc_final: 0.7410 (m100) outliers start: 18 outliers final: 14 residues processed: 151 average time/residue: 0.1367 time to fit residues: 30.5316 Evaluate side-chains 148 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 118 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 157 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.067945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.049969 restraints weight = 91111.717| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 4.99 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15288 Z= 0.130 Angle : 0.534 12.217 20836 Z= 0.261 Chirality : 0.041 0.219 2438 Planarity : 0.003 0.043 2520 Dihedral : 6.871 56.741 2636 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.07 % Allowed : 9.63 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.58 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: 1.08 (0.21), residues: 1755 helix: 2.32 (0.21), residues: 567 sheet: -0.47 (0.26), residues: 456 loop : 0.39 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 136 TYR 0.022 0.001 TYR E 299 PHE 0.015 0.001 PHE C 417 TRP 0.012 0.001 TRP E 426 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00289 (15250) covalent geometry : angle 0.52515 (20728) SS BOND : bond 0.00064 ( 6) SS BOND : angle 0.45842 ( 12) hydrogen bonds : bond 0.03741 ( 525) hydrogen bonds : angle 4.29886 ( 1463) link_ALPHA1-2 : bond 0.00983 ( 3) link_ALPHA1-2 : angle 1.37442 ( 9) link_ALPHA1-3 : bond 0.00918 ( 7) link_ALPHA1-3 : angle 1.88040 ( 21) link_ALPHA1-6 : bond 0.00592 ( 5) link_ALPHA1-6 : angle 1.89198 ( 15) link_BETA1-4 : bond 0.00346 ( 10) link_BETA1-4 : angle 1.33221 ( 30) link_NAG-ASN : bond 0.00162 ( 7) link_NAG-ASN : angle 1.22208 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.9053 (mtp) cc_final: 0.8430 (mtp) REVERT: A 122 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8220 (p) REVERT: A 141 MET cc_start: 0.8916 (mtt) cc_final: 0.8406 (mtt) REVERT: A 266 MET cc_start: 0.9255 (mmm) cc_final: 0.8965 (tpt) REVERT: A 293 CYS cc_start: 0.9057 (m) cc_final: 0.8530 (m) REVERT: B 61 MET cc_start: 0.9197 (ptp) cc_final: 0.8825 (ptp) REVERT: B 155 GLU cc_start: 0.7408 (mp0) cc_final: 0.7108 (mp0) REVERT: B 182 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8554 (mm-30) REVERT: B 261 MET cc_start: 0.9494 (mmm) cc_final: 0.9106 (mmm) REVERT: B 270 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8551 (mm-30) REVERT: B 298 GLU cc_start: 0.9242 (tm-30) cc_final: 0.8976 (tm-30) REVERT: C 70 MET cc_start: 0.9341 (mmt) cc_final: 0.8832 (mmm) REVERT: C 189 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7169 (mm-30) REVERT: C 239 GLN cc_start: 0.8648 (mm110) cc_final: 0.8310 (tt0) REVERT: D 81 MET cc_start: 0.8325 (pmm) cc_final: 0.8097 (pmm) REVERT: D 114 MET cc_start: 0.8880 (mmm) cc_final: 0.8559 (mmm) REVERT: D 258 PHE cc_start: 0.8842 (t80) cc_final: 0.8494 (t80) REVERT: D 266 MET cc_start: 0.8923 (tpp) cc_final: 0.8578 (tpp) REVERT: D 288 TRP cc_start: 0.7426 (m100) cc_final: 0.6968 (m-10) REVERT: E 90 GLN cc_start: 0.9459 (mt0) cc_final: 0.8638 (mp10) REVERT: E 115 MET cc_start: 0.8487 (ptp) cc_final: 0.8173 (ptm) REVERT: E 237 TRP cc_start: 0.9101 (m-10) cc_final: 0.8733 (m-10) REVERT: E 267 HIS cc_start: 0.8579 (m90) cc_final: 0.8064 (m90) REVERT: E 269 ARG cc_start: 0.8519 (tpp-160) cc_final: 0.8062 (tpp-160) REVERT: E 286 MET cc_start: 0.8874 (tpt) cc_final: 0.8668 (tpt) REVERT: F 435 THR cc_start: 0.7831 (m) cc_final: 0.7510 (t) REVERT: F 445 ARG cc_start: 0.8213 (ttp-170) cc_final: 0.7841 (tmm-80) REVERT: F 446 GLN cc_start: 0.8573 (pp30) cc_final: 0.7908 (tp40) REVERT: F 455 LEU cc_start: 0.7915 (mm) cc_final: 0.7663 (mm) REVERT: F 458 MET cc_start: 0.5647 (ttm) cc_final: 0.4806 (ttm) REVERT: F 462 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7876 (mtm180) REVERT: F 473 ARG cc_start: 0.8977 (mtm180) cc_final: 0.8088 (ptt180) REVERT: F 474 PHE cc_start: 0.8492 (m-10) cc_final: 0.8280 (m-10) REVERT: F 475 THR cc_start: 0.8512 (m) cc_final: 0.8059 (p) REVERT: F 479 ASP cc_start: 0.8021 (t0) cc_final: 0.7561 (t0) REVERT: F 482 LYS cc_start: 0.9488 (mtpp) cc_final: 0.8969 (mtmm) REVERT: F 488 GLN cc_start: 0.8274 (tp40) cc_final: 0.7568 (tm-30) REVERT: F 509 TRP cc_start: 0.8463 (m100) cc_final: 0.8256 (m100) REVERT: F 520 TRP cc_start: 0.8098 (m100) cc_final: 0.7422 (m100) outliers start: 17 outliers final: 14 residues processed: 150 average time/residue: 0.1319 time to fit residues: 29.7388 Evaluate side-chains 149 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 74 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.068025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.049954 restraints weight = 97480.368| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 5.16 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15288 Z= 0.131 Angle : 0.545 12.165 20836 Z= 0.263 Chirality : 0.041 0.224 2438 Planarity : 0.003 0.042 2520 Dihedral : 6.605 55.813 2636 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.32 % Allowed : 9.76 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.58 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: 1.13 (0.21), residues: 1755 helix: 2.38 (0.21), residues: 565 sheet: -0.45 (0.26), residues: 456 loop : 0.41 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 136 TYR 0.024 0.001 TYR B 299 PHE 0.012 0.001 PHE C 308 TRP 0.011 0.001 TRP E 426 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00292 (15250) covalent geometry : angle 0.53613 (20728) SS BOND : bond 0.00059 ( 6) SS BOND : angle 0.45633 ( 12) hydrogen bonds : bond 0.03660 ( 525) hydrogen bonds : angle 4.26064 ( 1463) link_ALPHA1-2 : bond 0.00970 ( 3) link_ALPHA1-2 : angle 1.33883 ( 9) link_ALPHA1-3 : bond 0.00894 ( 7) link_ALPHA1-3 : angle 1.87192 ( 21) link_ALPHA1-6 : bond 0.00622 ( 5) link_ALPHA1-6 : angle 1.91754 ( 15) link_BETA1-4 : bond 0.00357 ( 10) link_BETA1-4 : angle 1.34093 ( 30) link_NAG-ASN : bond 0.00181 ( 7) link_NAG-ASN : angle 1.22252 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.9066 (mtp) cc_final: 0.8435 (mtp) REVERT: A 122 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8230 (p) REVERT: A 141 MET cc_start: 0.8926 (mtt) cc_final: 0.8418 (mtt) REVERT: A 266 MET cc_start: 0.9262 (mmm) cc_final: 0.8955 (tpt) REVERT: A 293 CYS cc_start: 0.9045 (m) cc_final: 0.8513 (m) REVERT: B 61 MET cc_start: 0.9087 (ptp) cc_final: 0.8714 (ptp) REVERT: B 155 GLU cc_start: 0.7420 (mp0) cc_final: 0.7115 (mp0) REVERT: B 182 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8590 (mm-30) REVERT: B 261 MET cc_start: 0.9516 (mmm) cc_final: 0.9139 (mmm) REVERT: B 270 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8553 (mm-30) REVERT: B 298 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8941 (tm-30) REVERT: C 70 MET cc_start: 0.9345 (mmt) cc_final: 0.8845 (mmm) REVERT: C 189 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7164 (mm-30) REVERT: C 239 GLN cc_start: 0.8668 (mm110) cc_final: 0.8375 (tt0) REVERT: D 114 MET cc_start: 0.8891 (mmm) cc_final: 0.8526 (mmm) REVERT: D 266 MET cc_start: 0.8927 (tpp) cc_final: 0.8582 (tpp) REVERT: D 288 TRP cc_start: 0.7365 (m100) cc_final: 0.6899 (m-10) REVERT: E 9 MET cc_start: 0.8535 (ttt) cc_final: 0.7613 (tpp) REVERT: E 90 GLN cc_start: 0.9457 (mt0) cc_final: 0.8792 (mm110) REVERT: E 115 MET cc_start: 0.8485 (ptp) cc_final: 0.8180 (ptm) REVERT: E 153 GLU cc_start: 0.8709 (mm-30) cc_final: 0.7572 (mm-30) REVERT: E 237 TRP cc_start: 0.9135 (m-10) cc_final: 0.8762 (m-10) REVERT: E 267 HIS cc_start: 0.8574 (m90) cc_final: 0.8213 (m-70) REVERT: E 269 ARG cc_start: 0.8534 (tpp-160) cc_final: 0.8020 (tpp-160) REVERT: F 435 THR cc_start: 0.7824 (m) cc_final: 0.7501 (t) REVERT: F 445 ARG cc_start: 0.8213 (ttp-170) cc_final: 0.7807 (tmm-80) REVERT: F 446 GLN cc_start: 0.8411 (pp30) cc_final: 0.7772 (tp40) REVERT: F 455 LEU cc_start: 0.7995 (mm) cc_final: 0.7759 (mm) REVERT: F 458 MET cc_start: 0.5870 (ttm) cc_final: 0.4998 (ttm) REVERT: F 462 ARG cc_start: 0.8149 (mtp85) cc_final: 0.7887 (mtm180) REVERT: F 473 ARG cc_start: 0.8968 (mtm180) cc_final: 0.8183 (ptt180) REVERT: F 474 PHE cc_start: 0.8379 (m-10) cc_final: 0.8147 (m-10) REVERT: F 475 THR cc_start: 0.8497 (m) cc_final: 0.8032 (p) REVERT: F 479 ASP cc_start: 0.8025 (t0) cc_final: 0.7543 (t0) REVERT: F 482 LYS cc_start: 0.9480 (mtpp) cc_final: 0.8957 (mtmm) REVERT: F 488 GLN cc_start: 0.8139 (tp40) cc_final: 0.7410 (tm-30) REVERT: F 509 TRP cc_start: 0.8475 (m100) cc_final: 0.8254 (m100) REVERT: F 512 ARG cc_start: 0.8235 (mmt180) cc_final: 0.8018 (mmt180) REVERT: F 520 TRP cc_start: 0.8088 (m100) cc_final: 0.7436 (m100) outliers start: 21 outliers final: 18 residues processed: 156 average time/residue: 0.1280 time to fit residues: 30.0388 Evaluate side-chains 155 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain F residue 5 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 113 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 45 optimal weight: 0.4980 chunk 85 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.068391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.050169 restraints weight = 83633.940| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 4.91 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2864 r_free = 0.2864 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15288 Z= 0.128 Angle : 0.555 12.221 20836 Z= 0.268 Chirality : 0.041 0.230 2438 Planarity : 0.003 0.042 2520 Dihedral : 6.448 57.549 2636 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.20 % Allowed : 9.95 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.58 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: 1.18 (0.21), residues: 1755 helix: 2.41 (0.21), residues: 565 sheet: -0.39 (0.26), residues: 458 loop : 0.42 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 85 TYR 0.021 0.001 TYR E 299 PHE 0.015 0.001 PHE C 417 TRP 0.011 0.001 TRP E 426 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00286 (15250) covalent geometry : angle 0.54640 (20728) SS BOND : bond 0.00057 ( 6) SS BOND : angle 0.48006 ( 12) hydrogen bonds : bond 0.03619 ( 525) hydrogen bonds : angle 4.23852 ( 1463) link_ALPHA1-2 : bond 0.00880 ( 3) link_ALPHA1-2 : angle 1.27837 ( 9) link_ALPHA1-3 : bond 0.00886 ( 7) link_ALPHA1-3 : angle 1.84879 ( 21) link_ALPHA1-6 : bond 0.00618 ( 5) link_ALPHA1-6 : angle 1.89539 ( 15) link_BETA1-4 : bond 0.00360 ( 10) link_BETA1-4 : angle 1.32632 ( 30) link_NAG-ASN : bond 0.00171 ( 7) link_NAG-ASN : angle 1.22353 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.9104 (mtp) cc_final: 0.8470 (mtp) REVERT: A 122 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8232 (p) REVERT: A 141 MET cc_start: 0.8918 (mtt) cc_final: 0.8382 (mtt) REVERT: A 266 MET cc_start: 0.9245 (mmm) cc_final: 0.8956 (tpt) REVERT: A 293 CYS cc_start: 0.9016 (m) cc_final: 0.8477 (m) REVERT: B 49 MET cc_start: 0.8408 (tpp) cc_final: 0.8072 (tpt) REVERT: B 61 MET cc_start: 0.9043 (ptp) cc_final: 0.8685 (ptp) REVERT: B 155 GLU cc_start: 0.7418 (mp0) cc_final: 0.7126 (mp0) REVERT: B 182 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8586 (mm-30) REVERT: B 261 MET cc_start: 0.9516 (mmm) cc_final: 0.9144 (mmm) REVERT: B 270 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8545 (mm-30) REVERT: B 298 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8963 (tm-30) REVERT: C 70 MET cc_start: 0.9349 (mmt) cc_final: 0.8850 (mmm) REVERT: C 189 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7161 (mm-30) REVERT: C 239 GLN cc_start: 0.8662 (mm110) cc_final: 0.8372 (tt0) REVERT: D 114 MET cc_start: 0.8854 (mmm) cc_final: 0.8598 (mmm) REVERT: D 266 MET cc_start: 0.8910 (tpp) cc_final: 0.8586 (tpp) REVERT: D 288 TRP cc_start: 0.7336 (m100) cc_final: 0.6875 (m-10) REVERT: E 9 MET cc_start: 0.8534 (ttt) cc_final: 0.7602 (tpp) REVERT: E 90 GLN cc_start: 0.9445 (mt0) cc_final: 0.8777 (mm110) REVERT: E 115 MET cc_start: 0.8479 (ptp) cc_final: 0.8169 (ptm) REVERT: E 153 GLU cc_start: 0.8704 (mm-30) cc_final: 0.7563 (mm-30) REVERT: E 237 TRP cc_start: 0.9126 (m-10) cc_final: 0.8758 (m-10) REVERT: E 267 HIS cc_start: 0.8527 (m90) cc_final: 0.8130 (m-70) REVERT: E 269 ARG cc_start: 0.8474 (tpp-160) cc_final: 0.7821 (tpp-160) REVERT: F 435 THR cc_start: 0.7772 (m) cc_final: 0.7379 (t) REVERT: F 445 ARG cc_start: 0.8116 (ttp-170) cc_final: 0.7750 (tmm-80) REVERT: F 446 GLN cc_start: 0.8377 (pp30) cc_final: 0.7766 (tp40) REVERT: F 455 LEU cc_start: 0.7923 (mm) cc_final: 0.7651 (mm) REVERT: F 458 MET cc_start: 0.5693 (ttm) cc_final: 0.4820 (ttm) REVERT: F 462 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7824 (mtm180) REVERT: F 475 THR cc_start: 0.8422 (m) cc_final: 0.7976 (p) REVERT: F 479 ASP cc_start: 0.8008 (t0) cc_final: 0.7452 (t0) REVERT: F 482 LYS cc_start: 0.9450 (mtpp) cc_final: 0.8934 (mtmm) REVERT: F 488 GLN cc_start: 0.8536 (tp40) cc_final: 0.7958 (tm-30) REVERT: F 509 TRP cc_start: 0.8458 (m100) cc_final: 0.8224 (m100) REVERT: F 512 ARG cc_start: 0.8260 (mmt180) cc_final: 0.7983 (mmt180) REVERT: F 517 TYR cc_start: 0.8249 (m-80) cc_final: 0.7616 (m-80) REVERT: F 520 TRP cc_start: 0.8026 (m100) cc_final: 0.7425 (m100) outliers start: 19 outliers final: 15 residues processed: 151 average time/residue: 0.1331 time to fit residues: 30.0398 Evaluate side-chains 152 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 29 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 35 optimal weight: 0.0370 chunk 100 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 107 optimal weight: 0.4980 chunk 126 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 154 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.067733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.050556 restraints weight = 57977.255| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 4.05 r_work: 0.2723 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15288 Z= 0.165 Angle : 0.572 12.370 20836 Z= 0.276 Chirality : 0.041 0.229 2438 Planarity : 0.003 0.041 2520 Dihedral : 6.409 59.803 2636 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.07 % Allowed : 10.20 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.58 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: 1.14 (0.21), residues: 1755 helix: 2.41 (0.21), residues: 565 sheet: -0.45 (0.25), residues: 460 loop : 0.40 (0.25), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 478 TYR 0.023 0.001 TYR E 299 PHE 0.014 0.001 PHE D 304 TRP 0.010 0.001 TRP E 426 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00369 (15250) covalent geometry : angle 0.56271 (20728) SS BOND : bond 0.00055 ( 6) SS BOND : angle 0.46101 ( 12) hydrogen bonds : bond 0.03777 ( 525) hydrogen bonds : angle 4.30282 ( 1463) link_ALPHA1-2 : bond 0.00890 ( 3) link_ALPHA1-2 : angle 1.34182 ( 9) link_ALPHA1-3 : bond 0.00864 ( 7) link_ALPHA1-3 : angle 1.90680 ( 21) link_ALPHA1-6 : bond 0.00593 ( 5) link_ALPHA1-6 : angle 1.99367 ( 15) link_BETA1-4 : bond 0.00329 ( 10) link_BETA1-4 : angle 1.39001 ( 30) link_NAG-ASN : bond 0.00223 ( 7) link_NAG-ASN : angle 1.34232 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.9365 (mtp) cc_final: 0.8784 (mtp) REVERT: A 122 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8104 (p) REVERT: A 141 MET cc_start: 0.9026 (mtt) cc_final: 0.8512 (mtt) REVERT: A 266 MET cc_start: 0.9636 (mmm) cc_final: 0.9296 (tpt) REVERT: A 293 CYS cc_start: 0.9241 (m) cc_final: 0.8775 (m) REVERT: B 49 MET cc_start: 0.8801 (tpp) cc_final: 0.8507 (tpt) REVERT: B 61 MET cc_start: 0.9389 (ptp) cc_final: 0.9078 (ptp) REVERT: B 155 GLU cc_start: 0.7806 (mp0) cc_final: 0.7562 (mp0) REVERT: B 182 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8857 (mm-30) REVERT: B 261 MET cc_start: 0.9633 (mmm) cc_final: 0.9294 (mmm) REVERT: B 270 GLU cc_start: 0.9403 (mt-10) cc_final: 0.8826 (mm-30) REVERT: B 298 GLU cc_start: 0.9434 (tm-30) cc_final: 0.9114 (tm-30) REVERT: C 70 MET cc_start: 0.9451 (mmt) cc_final: 0.8990 (mmm) REVERT: C 189 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7741 (mm-30) REVERT: C 199 TYR cc_start: 0.7945 (m-80) cc_final: 0.7370 (m-80) REVERT: C 239 GLN cc_start: 0.8909 (mm110) cc_final: 0.8595 (tt0) REVERT: D 58 MET cc_start: 0.9307 (mtt) cc_final: 0.8931 (mmm) REVERT: D 266 MET cc_start: 0.9150 (tpp) cc_final: 0.8781 (tpp) REVERT: D 288 TRP cc_start: 0.7589 (m100) cc_final: 0.7091 (m-10) REVERT: E 9 MET cc_start: 0.8513 (ttt) cc_final: 0.7594 (tpp) REVERT: E 90 GLN cc_start: 0.9461 (mt0) cc_final: 0.8874 (mm110) REVERT: E 115 MET cc_start: 0.8926 (ptp) cc_final: 0.8570 (ptm) REVERT: E 153 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8080 (mm-30) REVERT: E 237 TRP cc_start: 0.9294 (m-10) cc_final: 0.8883 (m-10) REVERT: E 267 HIS cc_start: 0.8667 (m90) cc_final: 0.8327 (m-70) REVERT: E 269 ARG cc_start: 0.8601 (tpp-160) cc_final: 0.7996 (tpp-160) REVERT: F 435 THR cc_start: 0.8203 (m) cc_final: 0.7706 (t) REVERT: F 445 ARG cc_start: 0.8201 (ttp-170) cc_final: 0.7514 (tmm-80) REVERT: F 446 GLN cc_start: 0.8400 (pp30) cc_final: 0.7723 (tp40) REVERT: F 455 LEU cc_start: 0.7922 (mm) cc_final: 0.7626 (mm) REVERT: F 458 MET cc_start: 0.5991 (ttm) cc_final: 0.5248 (ttm) REVERT: F 462 ARG cc_start: 0.8032 (mtp85) cc_final: 0.7702 (mtm180) REVERT: F 475 THR cc_start: 0.8453 (m) cc_final: 0.7971 (p) REVERT: F 479 ASP cc_start: 0.8184 (t0) cc_final: 0.7634 (t0) REVERT: F 482 LYS cc_start: 0.9464 (mtpp) cc_final: 0.8897 (mtmm) REVERT: F 488 GLN cc_start: 0.8517 (tp40) cc_final: 0.7874 (tm-30) REVERT: F 509 TRP cc_start: 0.8247 (m100) cc_final: 0.8007 (m100) REVERT: F 512 ARG cc_start: 0.8265 (mmt180) cc_final: 0.7839 (mmt180) REVERT: F 520 TRP cc_start: 0.8075 (m100) cc_final: 0.7421 (m100) outliers start: 17 outliers final: 16 residues processed: 149 average time/residue: 0.1319 time to fit residues: 29.5190 Evaluate side-chains 151 residues out of total 1586 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 282 TYR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 224 GLN Chi-restraints excluded: chain E residue 278 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 103 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 159 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 224 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.067976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.050168 restraints weight = 81894.591| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 4.77 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15288 Z= 0.131 Angle : 0.563 12.653 20836 Z= 0.272 Chirality : 0.041 0.231 2438 Planarity : 0.003 0.042 2520 Dihedral : 6.303 58.907 2636 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.20 % Allowed : 10.20 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.58 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: 1.16 (0.21), residues: 1755 helix: 2.40 (0.21), residues: 565 sheet: -0.40 (0.25), residues: 462 loop : 0.41 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 136 TYR 0.022 0.001 TYR E 299 PHE 0.015 0.001 PHE C 417 TRP 0.011 0.001 TRP E 426 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00292 (15250) covalent geometry : angle 0.55400 (20728) SS BOND : bond 0.00051 ( 6) SS BOND : angle 0.42036 ( 12) hydrogen bonds : bond 0.03693 ( 525) hydrogen bonds : angle 4.26605 ( 1463) link_ALPHA1-2 : bond 0.00875 ( 3) link_ALPHA1-2 : angle 1.31953 ( 9) link_ALPHA1-3 : bond 0.00914 ( 7) link_ALPHA1-3 : angle 1.86888 ( 21) link_ALPHA1-6 : bond 0.00650 ( 5) link_ALPHA1-6 : angle 1.92912 ( 15) link_BETA1-4 : bond 0.00360 ( 10) link_BETA1-4 : angle 1.36861 ( 30) link_NAG-ASN : bond 0.00177 ( 7) link_NAG-ASN : angle 1.25505 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2985.47 seconds wall clock time: 52 minutes 21.54 seconds (3141.54 seconds total)