Starting phenix.real_space_refine on Fri Oct 23 16:21:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25tw_80374/10_2026/25tw_80374.cif Found real_map, /net/cci-nas-00/data/ceres_data/25tw_80374/10_2026/25tw_80374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25tw_80374/10_2026/25tw_80374.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25tw_80374/10_2026/25tw_80374.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25tw_80374/10_2026/25tw_80374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25tw_80374/10_2026/25tw_80374.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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 57 5.16 5 C 6479 2.51 5 N 1791 2.21 5 O 1988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10315 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 3968 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 26, 'TRANS': 503} Chain breaks: 2 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 10, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 142 Chain: "B" Number of atoms: 3896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3896 Classifications: {'peptide': 524} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 26, 'TRANS': 497} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 258 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 13, 'ARG:plan': 4, 'PHE:plan': 1, 'ASN:plan1': 5, 'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 136 Chain: "C" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1307 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 171} Chain breaks: 1 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'ARG:plan': 2, 'PHE:plan': 5, 'TRP:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "D" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 888 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 3, 'ARG:plan': 3, 'TYR:plan': 4, 'PHE:plan': 2, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 109 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" 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: "I" 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: "J" 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: "A" 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: "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 Time building chain proxies: 2.29, per 1000 atoms: 0.22 Number of scatterers: 10315 At special positions: 0 Unit cell: (82.467, 119.952, 153.153, 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 57 16.00 O 1988 8.00 N 1791 7.00 C 6479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 437 " distance=2.03 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 527 " - pdb=" SG CYS A 545 " distance=2.03 Simple disulfide: pdb=" SG CYS A 548 " - pdb=" SG CYS A 560 " distance=2.03 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 249 " - pdb=" SG CYS B 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 430 " - pdb=" SG CYS B 437 " distance=2.03 Simple disulfide: pdb=" SG CYS B 523 " - pdb=" SG CYS B 542 " distance=2.04 Simple disulfide: pdb=" SG CYS C 29 " - pdb=" SG CYS C 44 " distance=2.03 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 44 " 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 BETA1-3 " NAG E 2 " - " BMA E 3 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " BETA1-6 " NAG E 1 " - " FUC E 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1001 " - " ASN A 98 " " NAG A1002 " - " ASN A 458 " " NAG B1001 " - " ASN B 458 " " NAG B1002 " - " ASN B 98 " " NAG E 1 " - " ASN C 59 " " NAG F 1 " - " ASN C 85 " " NAG G 1 " - " ASN C 90 " " NAG H 1 " - " ASN D 59 " " NAG I 1 " - " ASN D 85 " " NAG J 1 " - " ASN D 90 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 373.3 milliseconds 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2504 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 17 sheets defined 30.1% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 75 through 92 removed outlier: 3.710A pdb=" N LEU A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 123 removed outlier: 3.795A pdb=" N VAL A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 removed outlier: 3.563A pdb=" N PHE A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 removed outlier: 3.531A pdb=" N LEU A 186 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 188 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 216 removed outlier: 3.700A pdb=" N GLN A 205 " --> pdb=" O PRO A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 245 removed outlier: 3.799A pdb=" N GLU A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 266 through 276 removed outlier: 4.396A pdb=" N ILE A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 303 removed outlier: 3.947A pdb=" N GLN A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 319 Processing helix chain 'A' and resid 320 through 326 removed outlier: 3.615A pdb=" N GLN A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 363 through 373 Processing helix chain 'A' and resid 395 through 400 removed outlier: 3.567A pdb=" N SER A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 430 Processing helix chain 'A' and resid 437 through 443 removed outlier: 3.511A pdb=" N GLU A 441 " --> pdb=" O CYS A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 453 removed outlier: 3.781A pdb=" N LEU A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 91 Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.708A pdb=" N LEU B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 118 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE B 122 " --> pdb=" O GLN B 118 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL B 123 " --> pdb=" O SER B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 172 removed outlier: 3.594A pdb=" N ILE B 168 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 removed outlier: 3.529A pdb=" N ASP B 188 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 217 removed outlier: 3.677A pdb=" N GLN B 205 " --> pdb=" O PRO B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 246 removed outlier: 3.673A pdb=" N GLU B 236 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 277 Processing helix chain 'B' and resid 288 through 302 removed outlier: 3.899A pdb=" N GLN B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 319 removed outlier: 3.629A pdb=" N GLY B 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER B 318 " --> pdb=" O SER B 315 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS B 319 " --> pdb=" O TRP B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 removed outlier: 3.551A pdb=" N ALA B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 373 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 407 through 430 Processing helix chain 'B' and resid 437 through 443 removed outlier: 4.186A pdb=" N GLU B 441 " --> pdb=" O CYS B 437 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 442 " --> pdb=" O PRO B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 454 removed outlier: 3.793A pdb=" N LEU B 448 " --> pdb=" O GLY B 444 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN B 454 " --> pdb=" O LYS B 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 83 removed outlier: 3.843A pdb=" N ARG C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 208 removed outlier: 3.976A pdb=" N TRP C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU C 205 " --> pdb=" O PHE C 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.708A pdb=" N ALA D 103 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE D 104 " --> pdb=" O ASP D 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 104' Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.820A pdb=" N VAL A 49 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ARG A 104 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 51 " --> pdb=" O ARG A 104 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU A 106 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY A 53 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 4.796A pdb=" N ASP A 69 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 144 removed outlier: 3.959A pdb=" N ARG B 135 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA5, first strand: chain 'A' and resid 249 through 256 removed outlier: 7.298A pdb=" N VAL A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLN A 252 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR A 223 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL A 254 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA A 282 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 334 through 338 removed outlier: 3.608A pdb=" N GLY A 496 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N GLN A 481 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU A 494 " --> pdb=" O GLN A 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 457 through 458 removed outlier: 3.681A pdb=" N PHE A 457 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AA9, first strand: chain 'A' and resid 568 through 569 removed outlier: 3.615A pdb=" N GLN A 577 " --> pdb=" O ARG A 568 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 42 through 45 removed outlier: 3.529A pdb=" N ALA B 103 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL B 49 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ARG B 104 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B 51 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU B 106 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY B 53 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR B 50 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY B 152 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ILE B 177 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL B 153 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 221 through 223 Processing sheet with id=AB3, first strand: chain 'B' and resid 334 through 338 removed outlier: 3.853A pdb=" N GLY B 496 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 456 through 458 removed outlier: 3.532A pdb=" N PHE B 457 " --> pdb=" O VAL B 465 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 535 through 536 removed outlier: 3.553A pdb=" N THR B 535 " --> pdb=" O THR B 544 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 30 through 32 removed outlier: 3.754A pdb=" N LEU C 41 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA C 42 " --> pdb=" O ARG C 66 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 90 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU C 89 " --> pdb=" O GLN C 114 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU C 137 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 74 through 75 removed outlier: 4.318A pdb=" N VAL C 75 " --> pdb=" O TYR C 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 30 through 32 removed outlier: 4.239A pdb=" N LEU D 41 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA D 42 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN D 90 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N LEU D 89 " --> pdb=" O GLN D 114 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU D 113 " --> pdb=" O TYR D 138 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 831 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.21 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: 3434 1.34 - 1.46: 2350 1.46 - 1.58: 4652 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 10512 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.41e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.558 -0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C1 NAG B1001 " pdb=" O5 NAG B1001 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.99e+00 ... (remaining 10507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 13980 1.43 - 2.86: 251 2.86 - 4.29: 43 4.29 - 5.73: 18 5.73 - 7.16: 7 Bond angle restraints: 14299 Sorted by residual: angle pdb=" N LEU C 89 " pdb=" CA LEU C 89 " pdb=" C LEU C 89 " ideal model delta sigma weight residual 107.93 112.43 -4.50 1.65e+00 3.67e-01 7.45e+00 angle pdb=" CB GLU B 370 " pdb=" CG GLU B 370 " pdb=" CD GLU B 370 " ideal model delta sigma weight residual 112.60 116.96 -4.36 1.70e+00 3.46e-01 6.59e+00 angle pdb=" CB PRO C 156 " pdb=" CG PRO C 156 " pdb=" CD PRO C 156 " ideal model delta sigma weight residual 106.10 98.94 7.16 3.20e+00 9.77e-02 5.00e+00 angle pdb=" C1 BMA E 3 " pdb=" O5 BMA E 3 " pdb=" C5 BMA E 3 " ideal model delta sigma weight residual 118.82 112.33 6.49 3.00e+00 1.11e-01 4.68e+00 angle pdb=" N PRO C 156 " pdb=" CD PRO C 156 " pdb=" CG PRO C 156 " ideal model delta sigma weight residual 103.20 100.00 3.20 1.50e+00 4.44e-01 4.54e+00 ... (remaining 14294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.31: 5715 19.31 - 38.61: 634 38.61 - 57.92: 149 57.92 - 77.23: 36 77.23 - 96.53: 13 Dihedral angle restraints: 6547 sinusoidal: 2651 harmonic: 3896 Sorted by residual: dihedral pdb=" CB CYS B 249 " pdb=" SG CYS B 249 " pdb=" SG CYS B 541 " pdb=" CB CYS B 541 " ideal model delta sinusoidal sigma weight residual 93.00 177.83 -84.83 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS A 523 " pdb=" SG CYS A 523 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 176.02 -83.02 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS A 563 " pdb=" SG CYS A 563 " pdb=" SG CYS A 576 " pdb=" CB CYS A 576 " ideal model delta sinusoidal sigma weight residual 93.00 28.49 64.51 1 1.00e+01 1.00e-02 5.47e+01 ... (remaining 6544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1424 0.056 - 0.111: 219 0.111 - 0.167: 23 0.167 - 0.223: 1 0.223 - 0.279: 4 Chirality restraints: 1671 Sorted by residual: chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 458 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN D 59 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1668 not shown) Planarity restraints: 1861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 90 " 0.001 2.00e-02 2.50e+03 2.06e-02 5.31e+00 pdb=" CG ASN C 90 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C 90 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN C 90 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 437 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO B 438 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 438 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 438 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 33 " -0.006 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" CD GLU D 33 " 0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU D 33 " -0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU D 33 " -0.008 2.00e-02 2.50e+03 ... (remaining 1858 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1926 2.77 - 3.31: 9941 3.31 - 3.84: 16588 3.84 - 4.37: 18587 4.37 - 4.90: 32427 Nonbonded interactions: 79469 Sorted by model distance: nonbonded pdb=" O GLN D 76 " pdb=" OG SER D 79 " model vdw 2.242 3.040 nonbonded pdb=" O ASP A 347 " pdb=" OG1 THR A 351 " model vdw 2.271 3.040 nonbonded pdb=" OG1 THR B 377 " pdb=" O LEU D 31 " model vdw 2.308 3.040 nonbonded pdb=" OD1 ASP B 48 " pdb=" OG1 THR B 100 " model vdw 2.309 3.040 nonbonded pdb=" OH TYR B 230 " pdb=" OG SER B 313 " model vdw 2.312 3.040 ... (remaining 79464 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 40 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 132 or (resid 133 and (name N o \ r name CA or name C or name O or name CB )) or resid 134 through 145 or (resid 1 \ 46 and (name N or name CA or name C or name O or name CB )) or resid 147 through \ 232 or (resid 233 and (name N or name CA or name C or name O or name CB )) or r \ esid 234 through 254 or (resid 255 and (name N or name CA or name C or name O or \ name CB )) or resid 256 through 257 or resid 264 through 266 or (resid 267 and \ (name N or name CA or name C or name O or name CB )) or resid 268 through 269 or \ (resid 270 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 1 or (resid 272 and (name N or name CA or name C or name O or name CB )) or resi \ d 273 through 277 or (resid 278 through 279 and (name N or name CA or name C or \ name O or name CB )) or resid 280 through 287 or (resid 288 through 291 and (nam \ e N or name CA or name C or name O or name CB )) or resid 292 or (resid 293 thro \ ugh 295 and (name N or name CA or name C or name O or name CB )) or resid 296 th \ rough 300 or (resid 301 through 305 and (name N or name CA or name C or name O o \ r name CB )) or resid 306 through 355 or (resid 356 and (name N or name CA or na \ me C or name O or name CB )) or resid 357 through 378 or (resid 379 and (name N \ or name CA or name C or name O or name CB )) or resid 380 through 381 or (resid \ 382 and (name N or name CA or name C or name O or name CB )) or resid 383 throug \ h 386 or (resid 387 and (name N or name CA or name C or name O or name CB )) or \ resid 388 through 485 or (resid 486 through 489 and (name N or name CA or name C \ or name O or name CB )) or resid 490 through 499 or (resid 500 and (name N or n \ ame CA or name C or name O or name CB )) or resid 501 through 524 or (resid 525 \ and (name N or name CA or name C or name O or name CB )) or resid 526 or resid 5 \ 29 through 550 or (resid 551 through 552 and (name N or name CA or name C or nam \ e O or name CB )) or resid 553 through 558 or resid 566 through 571 or (resid 57 \ 2 through 573 and (name N or name CA or name C or name O or name CB )) or resid \ 574 through 576 or (resid 577 and (name N or name CA or name C or name O or name \ CB )) or resid 1001 through 1002)) selection = (chain 'B' and (resid 40 through 47 or (resid 48 and (name N or name CA or name \ C or name O or name CB )) or resid 49 through 189 or (resid 190 and (name N or n \ ame CA or name C or name O or name CB )) or resid 191 through 268 or (resid 269 \ through 270 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 1 through 278 or (resid 279 and (name N or name CA or name C or name O or name C \ B )) or resid 280 through 318 or (resid 319 and (name N or name CA or name C or \ name O or name CB )) or resid 320 through 325 or (resid 326 through 328 and (nam \ e N or name CA or name C or name O or name CB )) or resid 329 through 383 or (re \ sid 384 through 385 and (name N or name CA or name C or name O or name CB )) or \ resid 386 through 484 or (resid 485 through 489 and (name N or name CA or name C \ or name O or name CB )) or resid 490 through 506 or (resid 507 and (name N or n \ ame CA or name C or name O or name CB )) or resid 508 through 512 or (resid 513 \ and (name N or name CA or name C or name O or name CB )) or resid 514 through 51 \ 6 or (resid 517 through 518 and (name N or name CA or name C or name O or name C \ B )) or resid 519 through 523 or (resid 524 through 525 and (name N or name CA o \ r name C or name O or name CB )) or resid 526 through 535 or resid 541 through 5 \ 45 or (resid 546 and (name N or name CA or name C or name O or name CB )) or res \ id 547 through 554 or (resid 555 through 566 and (name N or name CA or name C or \ name O or name CB )) or resid 567 through 570 or (resid 571 through 573 and (na \ me N or name CA or name C or name O or name CB )) or resid 574 through 577 or re \ sid 1001 through 1002)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.160 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10547 Z= 0.138 Angle : 0.522 8.740 14388 Z= 0.242 Chirality : 0.043 0.279 1671 Planarity : 0.003 0.053 1851 Dihedral : 17.150 96.532 3995 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.10 % Allowed : 29.73 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.23), residues: 1336 helix: 1.29 (0.27), residues: 372 sheet: -0.63 (0.44), residues: 167 loop : -1.35 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 73 TYR 0.009 0.000 TYR C 88 PHE 0.006 0.000 PHE A 308 TRP 0.009 0.001 TRP D 40 HIS 0.002 0.000 HIS B 307 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (10512) covalent geometry : angle 0.50286 / 0.24 (14299) SS BOND : bond 0.00180 / 0.13 ( 16) SS BOND : angle 0.48807 / 0.41 ( 32) hydrogen bonds : bond 0.22407 / 15.62 ( 290) hydrogen bonds : angle 6.88785 / 4.79 ( 831) link_BETA1-3 : bond 0.00478 / 0.32 ( 1) link_BETA1-3 : angle 1.35030 / 0.96 ( 3) link_BETA1-4 : bond 0.00526 / 0.26 ( 7) link_BETA1-4 : angle 1.09045 / 0.77 ( 21) link_BETA1-6 : bond 0.00547 / 0.36 ( 1) link_BETA1-6 : angle 1.09540 / 0.83 ( 3) link_NAG-ASN : bond 0.00702 / 0.38 ( 10) link_NAG-ASN : angle 2.95210 / 1.89 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 93 LYS cc_start: 0.8655 (mptt) cc_final: 0.8418 (mttp) outliers start: 1 outliers final: 1 residues processed: 145 average time/residue: 0.0889 time to fit residues: 18.6479 Evaluate side-chains 137 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 GLN A 307 HIS D 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.201885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.152080 restraints weight = 14225.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.152498 restraints weight = 10786.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.151984 restraints weight = 9504.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.152145 restraints weight = 9292.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.152220 restraints weight = 8640.997| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.0806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10547 Z= 0.100 Angle : 0.493 8.921 14388 Z= 0.247 Chirality : 0.042 0.342 1671 Planarity : 0.003 0.035 1851 Dihedral : 8.698 82.212 1844 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.40 % Allowed : 27.93 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.23), residues: 1336 helix: 1.55 (0.27), residues: 382 sheet: -0.78 (0.43), residues: 169 loop : -1.45 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 73 TYR 0.014 0.001 TYR C 77 PHE 0.009 0.001 PHE A 346 TRP 0.022 0.001 TRP B 511 HIS 0.002 0.000 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (10512) covalent geometry : angle 0.47106 / 0.24 (14299) SS BOND : bond 0.00180 / 0.12 ( 16) SS BOND : angle 0.51158 / 0.41 ( 32) hydrogen bonds : bond 0.04351 / 3.08 ( 290) hydrogen bonds : angle 4.99479 / 3.55 ( 831) link_BETA1-3 : bond 0.00246 / 0.16 ( 1) link_BETA1-3 : angle 3.34321 / 2.52 ( 3) link_BETA1-4 : bond 0.00487 / 0.26 ( 7) link_BETA1-4 : angle 1.74815 / 1.10 ( 21) link_BETA1-6 : bond 0.00237 / 0.16 ( 1) link_BETA1-6 : angle 1.36960 / 1.18 ( 3) link_NAG-ASN : bond 0.00724 / 0.41 ( 10) link_NAG-ASN : angle 2.68605 / 1.80 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.6117 (t80) REVERT: A 479 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7207 (mm) REVERT: B 149 LYS cc_start: 0.7634 (ptmt) cc_final: 0.7321 (pttm) REVERT: B 537 LYS cc_start: 0.6296 (mmtt) cc_final: 0.5400 (ptpp) REVERT: C 93 LYS cc_start: 0.8865 (mptt) cc_final: 0.8632 (mttp) REVERT: C 101 ASP cc_start: 0.5549 (OUTLIER) cc_final: 0.5157 (p0) REVERT: D 33 GLU cc_start: 0.7282 (pp20) cc_final: 0.7047 (pp20) outliers start: 24 outliers final: 15 residues processed: 172 average time/residue: 0.0900 time to fit residues: 22.4410 Evaluate side-chains 158 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 554 GLN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: [70, 93, 10, 107, 8, 50, 0, 37, 22, 51, 130] chunk 70 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 107 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 130 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN B 41 HIS B 424 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.195861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.144541 restraints weight = 14121.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.142234 restraints weight = 13664.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143592 restraints weight = 13336.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.143833 restraints weight = 11498.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.144171 restraints weight = 10204.497| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10547 Z= 0.164 Angle : 0.536 9.211 14388 Z= 0.268 Chirality : 0.043 0.352 1671 Planarity : 0.003 0.038 1851 Dihedral : 7.817 75.305 1842 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 5.81 % Allowed : 24.62 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.23), residues: 1336 helix: 1.34 (0.27), residues: 382 sheet: -0.79 (0.43), residues: 174 loop : -1.50 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 395 TYR 0.013 0.001 TYR B 179 PHE 0.014 0.001 PHE A 346 TRP 0.026 0.001 TRP B 511 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (10512) covalent geometry : angle 0.51476 / 0.26 (14299) SS BOND : bond 0.00224 / 0.16 ( 16) SS BOND : angle 0.74363 / 0.59 ( 32) hydrogen bonds : bond 0.04426 / 3.11 ( 290) hydrogen bonds : angle 4.73735 / 3.38 ( 831) link_BETA1-3 : bond 0.00274 / 0.18 ( 1) link_BETA1-3 : angle 2.79362 / 2.02 ( 3) link_BETA1-4 : bond 0.00342 / 0.21 ( 7) link_BETA1-4 : angle 1.96209 / 1.24 ( 21) link_BETA1-6 : bond 0.00241 / 0.16 ( 1) link_BETA1-6 : angle 1.16614 / 0.88 ( 3) link_NAG-ASN : bond 0.00643 / 0.35 ( 10) link_NAG-ASN : angle 2.73318 / 1.85 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 143 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.6491 (t80) REVERT: A 394 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6590 (pt0) REVERT: A 479 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7299 (mm) REVERT: B 74 ASN cc_start: 0.8376 (m-40) cc_final: 0.8002 (m110) REVERT: B 112 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7995 (p0) REVERT: B 149 LYS cc_start: 0.7852 (ptmt) cc_final: 0.7391 (pttm) REVERT: B 537 LYS cc_start: 0.6313 (mmtt) cc_final: 0.5510 (ptpp) REVERT: C 101 ASP cc_start: 0.5429 (OUTLIER) cc_final: 0.5094 (p0) REVERT: C 111 GLN cc_start: 0.7720 (tp40) cc_final: 0.7231 (tp40) REVERT: C 135 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7496 (mp0) REVERT: C 188 TYR cc_start: 0.5876 (OUTLIER) cc_final: 0.4925 (m-80) REVERT: D 70 ASN cc_start: 0.6709 (t0) cc_final: 0.6461 (t0) outliers start: 58 outliers final: 31 residues processed: 190 average time/residue: 0.0851 time to fit residues: 23.9221 Evaluate side-chains 166 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: [72, 116, 107, 45, 101, 51, 22, 23, 7, 99, 65] chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 22 optimal weight: 0.0050 chunk 23 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 570 ASN ** 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 = 0.4280 r_free = 0.4280 target = 0.188383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.132345 restraints weight = 14213.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.132383 restraints weight = 11879.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.132664 restraints weight = 10746.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.132629 restraints weight = 10564.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.132732 restraints weight = 9629.205| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10547 Z= 0.214 Angle : 0.584 9.735 14388 Z= 0.294 Chirality : 0.045 0.345 1671 Planarity : 0.004 0.040 1851 Dihedral : 7.299 64.779 1842 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.11 % Allowed : 26.93 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.22), residues: 1336 helix: 1.03 (0.26), residues: 383 sheet: -1.27 (0.39), residues: 181 loop : -1.58 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 71 TYR 0.016 0.001 TYR C 77 PHE 0.016 0.002 PHE A 346 TRP 0.030 0.002 TRP B 511 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.21 (10512) covalent geometry : angle 0.56102 / 0.29 (14299) SS BOND : bond 0.00724 / 0.43 ( 16) SS BOND : angle 1.03620 / 0.84 ( 32) hydrogen bonds : bond 0.04654 / 3.28 ( 290) hydrogen bonds : angle 4.79362 / 3.41 ( 831) link_BETA1-3 : bond 0.00341 / 0.23 ( 1) link_BETA1-3 : angle 1.85177 / 1.33 ( 3) link_BETA1-4 : bond 0.00401 / 0.22 ( 7) link_BETA1-4 : angle 2.09455 / 1.31 ( 21) link_BETA1-6 : bond 0.00232 / 0.15 ( 1) link_BETA1-6 : angle 1.17782 / 0.83 ( 3) link_NAG-ASN : bond 0.00806 / 0.51 ( 10) link_NAG-ASN : angle 2.93814 / 1.95 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 139 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.6881 (t80) REVERT: A 240 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7949 (mm-40) REVERT: A 394 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7203 (pt0) REVERT: A 479 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7572 (mm) REVERT: B 74 ASN cc_start: 0.8653 (m-40) cc_final: 0.8375 (m-40) REVERT: B 334 ILE cc_start: 0.7838 (pt) cc_final: 0.7515 (mt) REVERT: B 337 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7698 (pm20) REVERT: B 537 LYS cc_start: 0.6766 (mmtt) cc_final: 0.5863 (pttm) REVERT: C 101 ASP cc_start: 0.5866 (OUTLIER) cc_final: 0.5368 (p0) REVERT: C 188 TYR cc_start: 0.6102 (OUTLIER) cc_final: 0.5111 (m-80) REVERT: D 70 ASN cc_start: 0.7045 (t0) cc_final: 0.6632 (t0) outliers start: 51 outliers final: 32 residues processed: 183 average time/residue: 0.0874 time to fit residues: 23.4369 Evaluate side-chains 172 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 41 HIS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 393 GLN Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 163 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: [62, 32, 72, 0, 70, 128, 82, 132, 108, 107, 117] chunk 62 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 117 optimal weight: 0.0670 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 570 ASN ** 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 = 0.4359 r_free = 0.4359 target = 0.195593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.138803 restraints weight = 14306.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.139580 restraints weight = 11508.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.139446 restraints weight = 10657.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.139536 restraints weight = 9529.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.139949 restraints weight = 8997.035| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10547 Z= 0.132 Angle : 0.524 12.900 14388 Z= 0.260 Chirality : 0.043 0.331 1671 Planarity : 0.003 0.037 1851 Dihedral : 6.740 57.638 1842 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 5.01 % Allowed : 26.53 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.23), residues: 1336 helix: 1.16 (0.27), residues: 383 sheet: -1.25 (0.40), residues: 179 loop : -1.56 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 190 TYR 0.010 0.001 TYR C 98 PHE 0.010 0.001 PHE A 346 TRP 0.017 0.001 TRP B 310 HIS 0.002 0.001 HIS B 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (10512) covalent geometry : angle 0.49927 / 0.25 (14299) SS BOND : bond 0.00476 / 0.29 ( 16) SS BOND : angle 0.88841 / 0.65 ( 32) hydrogen bonds : bond 0.03915 / 2.75 ( 290) hydrogen bonds : angle 4.54919 / 3.25 ( 831) link_BETA1-3 : bond 0.00363 / 0.24 ( 1) link_BETA1-3 : angle 1.60851 / 1.17 ( 3) link_BETA1-4 : bond 0.00412 / 0.21 ( 7) link_BETA1-4 : angle 1.94126 / 1.23 ( 21) link_BETA1-6 : bond 0.00337 / 0.22 ( 1) link_BETA1-6 : angle 1.10301 / 0.82 ( 3) link_NAG-ASN : bond 0.00733 / 0.44 ( 10) link_NAG-ASN : angle 3.01444 / 2.10 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.6459 (t80) REVERT: A 240 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7948 (mm-40) REVERT: A 479 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7714 (mm) REVERT: B 74 ASN cc_start: 0.8651 (m-40) cc_final: 0.8329 (m110) REVERT: B 149 LYS cc_start: 0.7768 (ptmt) cc_final: 0.7412 (pttm) REVERT: B 334 ILE cc_start: 0.7813 (pt) cc_final: 0.7485 (mt) REVERT: B 537 LYS cc_start: 0.6964 (mmtt) cc_final: 0.5886 (pttm) REVERT: C 101 ASP cc_start: 0.6043 (OUTLIER) cc_final: 0.5425 (p0) REVERT: C 111 GLN cc_start: 0.7957 (tp40) cc_final: 0.7305 (tp40) REVERT: C 135 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7677 (mp0) REVERT: C 188 TYR cc_start: 0.6058 (OUTLIER) cc_final: 0.5120 (m-80) outliers start: 50 outliers final: 35 residues processed: 177 average time/residue: 0.0866 time to fit residues: 22.4355 Evaluate side-chains 171 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 542 CYS Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 163 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: [52, 8, 40, 108, 93, 83, 110, 105, 63, 15, 117] chunk 52 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 15 optimal weight: 0.3980 chunk 117 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 570 ASN ** 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 = 0.4352 r_free = 0.4352 target = 0.194791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.139392 restraints weight = 14384.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.140216 restraints weight = 10762.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.139495 restraints weight = 9179.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.139532 restraints weight = 9028.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139690 restraints weight = 8567.205| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10547 Z= 0.140 Angle : 0.524 10.065 14388 Z= 0.261 Chirality : 0.043 0.338 1671 Planarity : 0.003 0.039 1851 Dihedral : 6.114 54.995 1842 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.16 % Favored : 94.76 % Rotamer: Outliers : 5.41 % Allowed : 26.43 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.22), residues: 1336 helix: 1.03 (0.26), residues: 389 sheet: -1.29 (0.41), residues: 171 loop : -1.63 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 73 TYR 0.020 0.001 TYR C 77 PHE 0.011 0.001 PHE A 346 TRP 0.012 0.001 TRP B 511 HIS 0.002 0.000 HIS B 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (10512) covalent geometry : angle 0.49958 / 0.26 (14299) SS BOND : bond 0.00292 / 0.21 ( 16) SS BOND : angle 0.80873 / 0.58 ( 32) hydrogen bonds : bond 0.03846 / 2.71 ( 290) hydrogen bonds : angle 4.43071 / 3.16 ( 831) link_BETA1-3 : bond 0.00419 / 0.28 ( 1) link_BETA1-3 : angle 1.39569 / 1.02 ( 3) link_BETA1-4 : bond 0.00334 / 0.17 ( 7) link_BETA1-4 : angle 1.91708 / 1.20 ( 21) link_BETA1-6 : bond 0.00356 / 0.24 ( 1) link_BETA1-6 : angle 1.12289 / 0.80 ( 3) link_NAG-ASN : bond 0.00743 / 0.45 ( 10) link_NAG-ASN : angle 3.01877 / 2.11 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 135 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.6742 (t80) REVERT: A 240 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8248 (mm-40) REVERT: A 479 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7743 (mm) REVERT: A 497 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.7155 (pp30) REVERT: B 74 ASN cc_start: 0.8739 (m-40) cc_final: 0.8428 (m110) REVERT: B 105 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8575 (mt) REVERT: B 149 LYS cc_start: 0.7710 (ptmt) cc_final: 0.7326 (pttm) REVERT: B 334 ILE cc_start: 0.7880 (pt) cc_final: 0.7513 (mt) REVERT: B 337 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7652 (pm20) REVERT: B 537 LYS cc_start: 0.6912 (mmtt) cc_final: 0.6048 (pttm) REVERT: C 101 ASP cc_start: 0.5799 (OUTLIER) cc_final: 0.5466 (p0) REVERT: C 188 TYR cc_start: 0.6072 (OUTLIER) cc_final: 0.5084 (m-80) REVERT: D 70 ASN cc_start: 0.6735 (t0) cc_final: 0.6376 (t0) outliers start: 54 outliers final: 40 residues processed: 180 average time/residue: 0.0834 time to fit residues: 22.1660 Evaluate side-chains 177 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain B residue 41 HIS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 505 ASN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 542 CYS Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 163 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: [108, 60, 58, 113, 89, 16, 61, 73, 37, 120, 131] chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 58 optimal weight: 0.0070 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 73 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 570 ASN ** 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 = 0.4359 r_free = 0.4359 target = 0.195526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.141118 restraints weight = 14166.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.139961 restraints weight = 11104.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.139527 restraints weight = 9409.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.139688 restraints weight = 9292.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.139785 restraints weight = 9030.362| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10547 Z= 0.118 Angle : 0.515 9.165 14388 Z= 0.256 Chirality : 0.042 0.330 1671 Planarity : 0.003 0.034 1851 Dihedral : 5.622 54.995 1842 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 5.61 % Allowed : 26.63 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.22), residues: 1336 helix: 1.17 (0.27), residues: 386 sheet: -1.30 (0.41), residues: 169 loop : -1.62 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 73 TYR 0.010 0.001 TYR C 98 PHE 0.010 0.001 PHE C 38 TRP 0.009 0.001 TRP B 511 HIS 0.002 0.000 HIS B 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (10512) covalent geometry : angle 0.48979 / 0.25 (14299) SS BOND : bond 0.00225 / 0.17 ( 16) SS BOND : angle 0.67198 / 0.53 ( 32) hydrogen bonds : bond 0.03586 / 2.52 ( 290) hydrogen bonds : angle 4.30416 / 3.08 ( 831) link_BETA1-3 : bond 0.00403 / 0.27 ( 1) link_BETA1-3 : angle 1.44820 / 1.05 ( 3) link_BETA1-4 : bond 0.00346 / 0.18 ( 7) link_BETA1-4 : angle 1.86994 / 1.16 ( 21) link_BETA1-6 : bond 0.00405 / 0.27 ( 1) link_BETA1-6 : angle 1.08600 / 0.79 ( 3) link_NAG-ASN : bond 0.00763 / 0.48 ( 10) link_NAG-ASN : angle 3.07321 / 2.14 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 136 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.6605 (t80) REVERT: A 240 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8230 (mm-40) REVERT: A 479 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7730 (mm) REVERT: A 497 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7152 (pp30) REVERT: B 74 ASN cc_start: 0.8728 (m-40) cc_final: 0.8432 (m110) REVERT: B 105 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8524 (mt) REVERT: B 334 ILE cc_start: 0.7925 (pt) cc_final: 0.7541 (mt) REVERT: B 337 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7507 (pm20) REVERT: B 430 CYS cc_start: 0.6224 (OUTLIER) cc_final: 0.5663 (p) REVERT: C 101 ASP cc_start: 0.5505 (OUTLIER) cc_final: 0.5215 (p0) REVERT: C 135 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7686 (mp0) REVERT: C 188 TYR cc_start: 0.5971 (OUTLIER) cc_final: 0.4976 (m-80) REVERT: C 204 TRP cc_start: 0.6700 (t-100) cc_final: 0.6461 (t-100) REVERT: D 70 ASN cc_start: 0.6892 (t0) cc_final: 0.6470 (t0) outliers start: 56 outliers final: 43 residues processed: 182 average time/residue: 0.0833 time to fit residues: 22.6542 Evaluate side-chains 186 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 135 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain B residue 41 HIS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 542 CYS Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 163 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: [63, 73, 7, 54, 100, 68, 96, 74, 133, 15, 89] chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 100 optimal weight: 0.0670 chunk 68 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 133 optimal weight: 0.8980 chunk 15 optimal weight: 0.0470 chunk 89 optimal weight: 0.1980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.196140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.139856 restraints weight = 14145.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.140440 restraints weight = 12692.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.140519 restraints weight = 9959.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.140566 restraints weight = 9685.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.140796 restraints weight = 9231.427| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10547 Z= 0.107 Angle : 0.505 8.822 14388 Z= 0.250 Chirality : 0.042 0.331 1671 Planarity : 0.003 0.058 1851 Dihedral : 5.276 55.504 1842 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 5.61 % Allowed : 26.63 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.23), residues: 1336 helix: 1.22 (0.27), residues: 386 sheet: -1.29 (0.41), residues: 169 loop : -1.61 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 73 TYR 0.019 0.001 TYR C 77 PHE 0.010 0.001 PHE C 38 TRP 0.012 0.001 TRP D 40 HIS 0.001 0.000 HIS B 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (10512) covalent geometry : angle 0.48133 / 0.25 (14299) SS BOND : bond 0.00202 / 0.15 ( 16) SS BOND : angle 0.61289 / 0.48 ( 32) hydrogen bonds : bond 0.03441 / 2.42 ( 290) hydrogen bonds : angle 4.20284 / 3.01 ( 831) link_BETA1-3 : bond 0.00399 / 0.27 ( 1) link_BETA1-3 : angle 1.44601 / 1.05 ( 3) link_BETA1-4 : bond 0.00364 / 0.18 ( 7) link_BETA1-4 : angle 1.65810 / 1.06 ( 21) link_BETA1-6 : bond 0.00412 / 0.27 ( 1) link_BETA1-6 : angle 1.09495 / 0.80 ( 3) link_NAG-ASN : bond 0.00738 / 0.45 ( 10) link_NAG-ASN : angle 3.05181 / 2.12 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 137 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.6612 (t80) REVERT: A 240 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8235 (mm-40) REVERT: A 394 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6810 (pt0) REVERT: A 479 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7768 (mm) REVERT: A 497 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7143 (pp30) REVERT: A 548 CYS cc_start: 0.0821 (OUTLIER) cc_final: -0.1020 (m) REVERT: B 74 ASN cc_start: 0.8710 (m-40) cc_final: 0.8406 (m110) REVERT: B 105 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8568 (mt) REVERT: B 334 ILE cc_start: 0.7942 (pt) cc_final: 0.7555 (mt) REVERT: B 337 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7510 (pm20) REVERT: B 430 CYS cc_start: 0.6336 (OUTLIER) cc_final: 0.5816 (p) REVERT: C 41 LEU cc_start: 0.8430 (tp) cc_final: 0.8224 (tp) REVERT: C 101 ASP cc_start: 0.5321 (OUTLIER) cc_final: 0.5009 (p0) REVERT: C 135 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7664 (mp0) REVERT: C 188 TYR cc_start: 0.5956 (OUTLIER) cc_final: 0.4956 (m-80) REVERT: C 204 TRP cc_start: 0.6725 (t-100) cc_final: 0.6492 (t-100) REVERT: D 70 ASN cc_start: 0.6814 (t0) cc_final: 0.6446 (t0) outliers start: 56 outliers final: 41 residues processed: 184 average time/residue: 0.0854 time to fit residues: 23.1399 Evaluate side-chains 184 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 133 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain B residue 41 HIS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 430 CYS Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 542 CYS Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 163 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: [36, 117, 107, 32, 66, 42, 78, 9, 50, 24, 44] chunk 36 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 66 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.194705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.140910 restraints weight = 14167.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.141787 restraints weight = 11790.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.141768 restraints weight = 9694.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141997 restraints weight = 9011.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142074 restraints weight = 8748.201| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10547 Z= 0.135 Angle : 0.528 9.821 14388 Z= 0.264 Chirality : 0.043 0.336 1671 Planarity : 0.003 0.059 1851 Dihedral : 5.171 54.868 1842 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.01 % Favored : 94.91 % Rotamer: Outliers : 5.31 % Allowed : 26.83 % Favored : 67.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.22), residues: 1336 helix: 1.14 (0.27), residues: 386 sheet: -1.32 (0.41), residues: 167 loop : -1.61 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 73 TYR 0.014 0.001 TYR C 98 PHE 0.011 0.001 PHE A 346 TRP 0.009 0.001 TRP D 40 HIS 0.002 0.000 HIS B 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (10512) covalent geometry : angle 0.50601 / 0.26 (14299) SS BOND : bond 0.00259 / 0.20 ( 16) SS BOND : angle 0.69071 / 0.54 ( 32) hydrogen bonds : bond 0.03714 / 2.63 ( 290) hydrogen bonds : angle 4.25084 / 3.04 ( 831) link_BETA1-3 : bond 0.00328 / 0.22 ( 1) link_BETA1-3 : angle 1.48283 / 1.05 ( 3) link_BETA1-4 : bond 0.00409 / 0.20 ( 7) link_BETA1-4 : angle 1.61312 / 1.06 ( 21) link_BETA1-6 : bond 0.00407 / 0.27 ( 1) link_BETA1-6 : angle 1.09677 / 0.78 ( 3) link_NAG-ASN : bond 0.00743 / 0.44 ( 10) link_NAG-ASN : angle 3.03868 / 2.11 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.6638 (t80) REVERT: A 232 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7534 (tm-30) REVERT: A 240 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8280 (mm-40) REVERT: A 479 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7799 (mm) REVERT: A 497 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7130 (pp30) REVERT: A 548 CYS cc_start: 0.0688 (OUTLIER) cc_final: -0.1111 (m) REVERT: B 74 ASN cc_start: 0.8753 (m-40) cc_final: 0.8445 (m110) REVERT: B 334 ILE cc_start: 0.7896 (pt) cc_final: 0.7594 (mt) REVERT: B 337 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: B 537 LYS cc_start: 0.6398 (mmtm) cc_final: 0.5532 (pttm) REVERT: C 135 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7685 (mp0) REVERT: C 188 TYR cc_start: 0.5936 (OUTLIER) cc_final: 0.4925 (m-80) REVERT: C 204 TRP cc_start: 0.6769 (t-100) cc_final: 0.6569 (t-100) REVERT: D 70 ASN cc_start: 0.6797 (t0) cc_final: 0.6473 (t0) outliers start: 53 outliers final: 42 residues processed: 180 average time/residue: 0.0843 time to fit residues: 22.3863 Evaluate side-chains 181 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 133 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain B residue 41 HIS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 542 CYS Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 163 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: [77, 15, 76, 58, 59, 109, 23, 89, 3, 131, 1] chunk 77 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 76 optimal weight: 7.9990 chunk 58 optimal weight: 0.0270 chunk 59 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 131 optimal weight: 20.0000 chunk 1 optimal weight: 0.5980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 570 ASN ** 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 = 0.4364 r_free = 0.4364 target = 0.196345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.147243 restraints weight = 14115.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.144372 restraints weight = 14251.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.147283 restraints weight = 14540.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.147734 restraints weight = 10347.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.147451 restraints weight = 9795.115| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10547 Z= 0.105 Angle : 0.519 14.465 14388 Z= 0.255 Chirality : 0.042 0.328 1671 Planarity : 0.003 0.060 1851 Dihedral : 5.085 55.358 1842 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.90 % Allowed : 27.43 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.23), residues: 1336 helix: 1.21 (0.27), residues: 386 sheet: -1.32 (0.41), residues: 167 loop : -1.58 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 73 TYR 0.021 0.001 TYR C 77 PHE 0.009 0.001 PHE C 38 TRP 0.009 0.001 TRP B 511 HIS 0.001 0.000 HIS B 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (10512) covalent geometry : angle 0.49792 / 0.25 (14299) SS BOND : bond 0.00204 / 0.15 ( 16) SS BOND : angle 0.60914 / 0.49 ( 32) hydrogen bonds : bond 0.03348 / 2.35 ( 290) hydrogen bonds : angle 4.15940 / 2.97 ( 831) link_BETA1-3 : bond 0.00408 / 0.27 ( 1) link_BETA1-3 : angle 1.45513 / 1.07 ( 3) link_BETA1-4 : bond 0.00407 / 0.20 ( 7) link_BETA1-4 : angle 1.40854 / 0.92 ( 21) link_BETA1-6 : bond 0.00476 / 0.32 ( 1) link_BETA1-6 : angle 1.08067 / 0.78 ( 3) link_NAG-ASN : bond 0.00740 / 0.45 ( 10) link_NAG-ASN : angle 3.00951 / 2.09 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 136 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.6553 (t80) REVERT: A 394 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6785 (pt0) REVERT: A 479 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7785 (mm) REVERT: A 497 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.7148 (pp30) REVERT: A 548 CYS cc_start: 0.0558 (OUTLIER) cc_final: -0.1243 (m) REVERT: B 74 ASN cc_start: 0.8760 (m-40) cc_final: 0.8443 (m110) REVERT: B 105 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8545 (mt) REVERT: B 334 ILE cc_start: 0.8080 (pt) cc_final: 0.7661 (mt) REVERT: B 337 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7593 (pm20) REVERT: B 537 LYS cc_start: 0.6333 (mmtm) cc_final: 0.5761 (pttm) REVERT: C 188 TYR cc_start: 0.5770 (OUTLIER) cc_final: 0.4810 (m-80) REVERT: D 33 GLU cc_start: 0.7369 (pp20) cc_final: 0.6769 (pp20) REVERT: D 70 ASN cc_start: 0.6720 (t0) cc_final: 0.6449 (t0) outliers start: 49 outliers final: 40 residues processed: 175 average time/residue: 0.0946 time to fit residues: 23.9950 Evaluate side-chains 173 residues out of total 1165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ASN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 369 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 394 GLU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 470 ASN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 497 GLN Chi-restraints excluded: chain A residue 548 CYS Chi-restraints excluded: chain B residue 41 HIS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 458 ASN Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 542 CYS Chi-restraints excluded: chain B residue 555 PHE Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 188 TYR Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 163 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: [10, 127, 11, 107, 42, 54, 35, 49, 70, 87, 61] chunk 10 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 0.0470 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 87 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 570 ASN ** 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 = 0.4364 r_free = 0.4364 target = 0.196240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.146744 restraints weight = 14147.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.143057 restraints weight = 13129.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.145196 restraints weight = 12817.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.145149 restraints weight = 10554.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.145115 restraints weight = 10306.197| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10547 Z= 0.105 Angle : 0.524 13.425 14388 Z= 0.258 Chirality : 0.042 0.331 1671 Planarity : 0.003 0.060 1851 Dihedral : 5.043 55.265 1842 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.11 % Allowed : 27.23 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.23), residues: 1336 helix: 1.21 (0.27), residues: 386 sheet: -1.30 (0.41), residues: 167 loop : -1.58 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 190 TYR 0.014 0.001 TYR C 98 PHE 0.008 0.001 PHE A 346 TRP 0.038 0.001 TRP C 204 HIS 0.001 0.000 HIS B 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (10512) covalent geometry : angle 0.50310 / 0.25 (14299) SS BOND : bond 0.00202 / 0.15 ( 16) SS BOND : angle 0.58381 / 0.48 ( 32) hydrogen bonds : bond 0.03322 / 2.33 ( 290) hydrogen bonds : angle 4.13525 / 2.95 ( 831) link_BETA1-3 : bond 0.00386 / 0.26 ( 1) link_BETA1-3 : angle 1.45779 / 1.06 ( 3) link_BETA1-4 : bond 0.00409 / 0.20 ( 7) link_BETA1-4 : angle 1.40577 / 0.93 ( 21) link_BETA1-6 : bond 0.00460 / 0.31 ( 1) link_BETA1-6 : angle 1.08453 / 0.77 ( 3) link_NAG-ASN : bond 0.00736 / 0.45 ( 10) link_NAG-ASN : angle 2.96783 / 2.05 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1862.97 seconds wall clock time: 32 minutes 47.76 seconds (1967.76 seconds total)