Starting phenix.real_space_refine on Tue Aug 26 20:54:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dmq_47013/08_2025/9dmq_47013_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dmq_47013/08_2025/9dmq_47013.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dmq_47013/08_2025/9dmq_47013_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dmq_47013/08_2025/9dmq_47013_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dmq_47013/08_2025/9dmq_47013.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dmq_47013/08_2025/9dmq_47013.map" } resolution = 2.06 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 86 5.16 5 C 13407 2.51 5 N 3287 2.21 5 O 3853 1.98 5 H 19838 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40475 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 6436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 6436 Classifications: {'peptide': 399} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 378} Chain breaks: 1 Chain: "C" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 6487 Classifications: {'peptide': 401} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 380} Chain breaks: 1 Chain: "E" Number of atoms: 6576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6576 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 379} Chain breaks: 3 Chain: "D" Number of atoms: 7054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 7054 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 402} Chain breaks: 1 Chain: "B" Number of atoms: 6482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6482 Classifications: {'peptide': 411} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 387} Chain breaks: 1 Chain: "F" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 3426 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 213} Chain breaks: 1 Chain: "G" Number of atoms: 3242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3242 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 199} Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "K" 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: "L" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" 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: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'CLR': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 190 Unusual residues: {'CLR': 3, 'NAG': 1, 'POV': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 101 Unusual residues: {'CLR': 2, 'POV': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 6.77, per 1000 atoms: 0.17 Number of scatterers: 40475 At special positions: 0 Unit cell: (102.85, 129.965, 227.205, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 86 16.00 P 4 15.00 O 3853 8.00 N 3287 7.00 C 13407 6.00 H 19838 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.05 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.05 Simple disulfide: pdb=" SG CYS D 130 " - pdb=" SG CYS D 144 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 470 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 191 " - pdb=" SG CYS F 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 42 " - pdb=" SG CYS G 108 " distance=2.04 Simple disulfide: pdb=" SG CYS G 155 " - pdb=" SG CYS G 215 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 7 " " MAN I 4 " - " MAN I 5 " " BMA J 3 " - " MAN J 6 " " MAN J 4 " - " MAN J 5 " " BMA L 3 " - " MAN L 6 " " MAN L 4 " - " MAN L 5 " " BMA N 3 " - " MAN N 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 4 " " MAN I 4 " - " MAN I 6 " " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " " BMA N 3 " - " MAN N 5 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG D 501 " - " ASN D 76 " " NAG H 1 " - " ASN A 141 " " NAG I 1 " - " ASN C 141 " " NAG J 1 " - " ASN E 141 " " NAG K 1 " - " ASN D 169 " " NAG L 1 " - " ASN D 143 " " NAG M 1 " - " ASN B 66 " " NAG N 1 " - " ASN B 141 " Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.2 microseconds 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4736 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 30 sheets defined 39.5% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.038A pdb=" N GLY A 73 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.557A pdb=" N LYS A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 218 through 230 removed outlier: 3.541A pdb=" N CYS A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 263 removed outlier: 3.932A pdb=" N LEU A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 319 through 324 removed outlier: 4.110A pdb=" N ILE A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 319 through 324' Processing helix chain 'A' and resid 369 through 436 removed outlier: 3.689A pdb=" N LYS A 373 " --> pdb=" O HIS A 369 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A 412 " --> pdb=" O HIS A 408 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLY A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.943A pdb=" N GLY C 73 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 218 through 231 removed outlier: 3.918A pdb=" N GLY C 230 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 235 Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'C' and resid 241 through 264 removed outlier: 3.848A pdb=" N LEU C 258 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 300 Processing helix chain 'C' and resid 309 through 317 Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.860A pdb=" N ASN C 322 " --> pdb=" O ASP C 318 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE C 323 " --> pdb=" O THR C 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 318 through 323' Processing helix chain 'C' and resid 369 through 436 removed outlier: 3.545A pdb=" N LYS C 373 " --> pdb=" O HIS C 369 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLY C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ARG C 429 " --> pdb=" O VAL C 425 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 222 through 229 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 251 Processing helix chain 'E' and resid 252 through 273 removed outlier: 3.865A pdb=" N ASP E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 311 Processing helix chain 'E' and resid 320 through 329 Processing helix chain 'E' and resid 329 through 335 removed outlier: 4.390A pdb=" N LEU E 333 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR E 334 " --> pdb=" O LYS E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 469 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 70 through 75 removed outlier: 3.902A pdb=" N GLY D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.524A pdb=" N VAL D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 255 through 276 removed outlier: 3.929A pdb=" N LYS D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 314 Processing helix chain 'D' and resid 323 through 333 removed outlier: 3.653A pdb=" N GLU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 339 Processing helix chain 'D' and resid 409 through 473 Proline residue: D 416 - end of helix removed outlier: 3.625A pdb=" N THR D 457 " --> pdb=" O LEU D 453 " (cutoff:3.500A) Proline residue: D 458 - end of helix removed outlier: 3.761A pdb=" N GLY D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.589A pdb=" N ARG B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 66 Processing helix chain 'B' and resid 68 through 73 removed outlier: 4.207A pdb=" N GLY B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 175 through 179 removed outlier: 4.113A pdb=" N TYR B 179 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 238 through 244 Processing helix chain 'B' and resid 251 through 272 removed outlier: 3.675A pdb=" N ASN B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 310 Processing helix chain 'B' and resid 319 through 328 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.582A pdb=" N ARG B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 459 removed outlier: 3.668A pdb=" N TRP B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 117 through 121 Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 238 through 241 removed outlier: 4.198A pdb=" N GLY F 241 " --> pdb=" O SER F 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 238 through 241' Processing helix chain 'F' and resid 252 through 255 Processing helix chain 'G' and resid 48 through 51 Processing helix chain 'G' and resid 99 through 103 removed outlier: 3.742A pdb=" N PHE G 103 " --> pdb=" O PRO G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 148 removed outlier: 3.798A pdb=" N SER G 148 " --> pdb=" O GLU G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 209 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.054A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.054A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A 53 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU A 40 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ARG A 55 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE A 38 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LYS A 57 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLN A 36 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLN A 59 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N GLY A 34 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N VAL A 61 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 9.739A pdb=" N THR A 32 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.335A pdb=" N THR A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU A 199 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR A 198 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER A 187 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP A 200 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR A 202 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY A 183 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N HIS A 204 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER A 181 " --> pdb=" O HIS A 204 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 206 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 80 removed outlier: 4.061A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 80 removed outlier: 4.061A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN C 53 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LEU C 40 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ARG C 55 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE C 38 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LYS C 57 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLN C 36 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLN C 59 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLY C 34 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N VAL C 61 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N THR C 32 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL C 29 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 31 " --> pdb=" O ASN C 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.924A pdb=" N THR C 148 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU C 199 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR C 198 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER C 187 " --> pdb=" O TYR C 198 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASP C 200 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS C 185 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR C 202 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY C 183 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N HIS C 204 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER C 181 " --> pdb=" O HIS C 204 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C 206 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.159A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 77 through 81 removed outlier: 4.159A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLU E 49 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU E 43 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER E 51 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR E 55 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU E 37 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP E 57 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N LEU E 35 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU E 59 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL E 33 " --> pdb=" O GLU E 59 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N THR E 61 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N VAL E 31 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N TYR E 63 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 13.394A pdb=" N VAL E 29 " --> pdb=" O TYR E 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 92 removed outlier: 6.902A pdb=" N ILE E 217 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.946A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLY D 116 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.946A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLY D 116 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR D 51 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER D 44 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR D 53 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU D 42 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN D 55 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR D 63 " --> pdb=" O ASP D 32 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASP D 32 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL D 31 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N SER D 161 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL D 33 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 92 through 94 removed outlier: 5.398A pdb=" N SER D 150 " --> pdb=" O GLN D 213 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLN D 213 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE D 220 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 92 through 94 removed outlier: 5.398A pdb=" N SER D 150 " --> pdb=" O GLN D 213 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLN D 213 " --> pdb=" O SER D 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 164 through 165 Processing sheet with id=AB7, first strand: chain 'B' and resid 77 through 81 Processing sheet with id=AB8, first strand: chain 'B' and resid 77 through 81 removed outlier: 6.190A pdb=" N THR B 49 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU B 43 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR B 51 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TRP B 55 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU B 37 " --> pdb=" O TRP B 55 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY B 57 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL B 35 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ASP B 59 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU B 33 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N GLN B 61 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE B 31 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.156A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE B 215 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.156A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 34 through 38 Processing sheet with id=AC3, first strand: chain 'F' and resid 42 through 43 removed outlier: 4.721A pdb=" N TYR F 64 " --> pdb=" O GLY F 129 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP F 65 " --> pdb=" O GLU F 81 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU F 81 " --> pdb=" O TRP F 65 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP F 67 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AC5, first strand: chain 'F' and resid 171 through 175 removed outlier: 5.176A pdb=" N ALA F 188 " --> pdb=" O VAL F 235 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL F 235 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY F 190 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL F 233 " --> pdb=" O GLY F 190 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU F 192 " --> pdb=" O SER F 231 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER F 231 " --> pdb=" O LEU F 192 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS F 194 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU F 229 " --> pdb=" O LYS F 194 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 171 through 175 removed outlier: 5.176A pdb=" N ALA F 188 " --> pdb=" O VAL F 235 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL F 235 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLY F 190 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL F 233 " --> pdb=" O GLY F 190 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU F 192 " --> pdb=" O SER F 231 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N SER F 231 " --> pdb=" O LEU F 192 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS F 194 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU F 229 " --> pdb=" O LYS F 194 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 202 through 205 Processing sheet with id=AC8, first strand: chain 'G' and resid 23 through 25 Processing sheet with id=AC9, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.343A pdb=" N LEU G 53 " --> pdb=" O TYR G 69 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR G 69 " --> pdb=" O LEU G 53 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP G 55 " --> pdb=" O LEU G 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 29 through 32 removed outlier: 4.105A pdb=" N THR G 118 " --> pdb=" O GLN G 110 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 135 through 139 removed outlier: 5.681A pdb=" N TYR G 194 " --> pdb=" O ASN G 159 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 174 through 175 1105 hydrogen bonds defined for protein. 3066 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: 9.58 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 19816 1.04 - 1.24: 2183 1.24 - 1.44: 6794 1.44 - 1.63: 12073 1.63 - 1.83: 132 Bond restraints: 40998 Sorted by residual: bond pdb=" ND2 ASN D 143 " pdb="HD21 ASN D 143 " ideal model delta sigma weight residual 0.860 0.973 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" ND2 ASN B 141 " pdb="HD21 ASN B 141 " ideal model delta sigma weight residual 0.860 0.973 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" ND2 ASN E 141 " pdb="HD21 ASN E 141 " ideal model delta sigma weight residual 0.860 0.973 -0.113 2.00e-02 2.50e+03 3.17e+01 bond pdb=" ND2 ASN A 141 " pdb="HD21 ASN A 141 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" ND2 ASN B 66 " pdb="HD21 ASN B 66 " ideal model delta sigma weight residual 0.860 0.969 -0.109 2.00e-02 2.50e+03 3.00e+01 ... (remaining 40993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.68: 73895 11.68 - 23.35: 1 23.35 - 35.03: 3 35.03 - 46.70: 0 46.70 - 58.38: 4 Bond angle restraints: 73903 Sorted by residual: angle pdb=" CA LEU C 366 " pdb=" N LEU C 366 " pdb=" H LEU C 366 " ideal model delta sigma weight residual 114.00 172.38 -58.38 3.00e+00 1.11e-01 3.79e+02 angle pdb=" CA GLY E 168 " pdb=" N GLY E 168 " pdb=" H GLY E 168 " ideal model delta sigma weight residual 114.00 171.15 -57.15 3.00e+00 1.11e-01 3.63e+02 angle pdb=" CA LEU E 407 " pdb=" N LEU E 407 " pdb=" H LEU E 407 " ideal model delta sigma weight residual 114.00 167.51 -53.51 3.00e+00 1.11e-01 3.18e+02 angle pdb=" CA GLY F 185 " pdb=" N GLY F 185 " pdb=" H GLY F 185 " ideal model delta sigma weight residual 114.00 161.42 -47.42 3.00e+00 1.11e-01 2.50e+02 angle pdb=" CA GLU E 206 " pdb=" N GLU E 206 " pdb=" H GLU E 206 " ideal model delta sigma weight residual 114.00 145.76 -31.76 3.00e+00 1.11e-01 1.12e+02 ... (remaining 73898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.97: 19602 33.97 - 67.94: 553 67.94 - 101.91: 71 101.91 - 135.88: 24 135.88 - 169.85: 1 Dihedral angle restraints: 20251 sinusoidal: 11465 harmonic: 8786 Sorted by residual: dihedral pdb=" CD ARG E 480 " pdb=" NE ARG E 480 " pdb=" CZ ARG E 480 " pdb=" NH1 ARG E 480 " ideal model delta sinusoidal sigma weight residual 0.00 71.34 -71.34 1 1.00e+01 1.00e-02 6.53e+01 dihedral pdb=" CD ARG E 28 " pdb=" NE ARG E 28 " pdb=" CZ ARG E 28 " pdb=" NH1 ARG E 28 " ideal model delta sinusoidal sigma weight residual 0.00 48.32 -48.32 1 1.00e+01 1.00e-02 3.22e+01 dihedral pdb=" CB CYS F 53 " pdb=" SG CYS F 53 " pdb=" SG CYS F 126 " pdb=" CB CYS F 126 " ideal model delta sinusoidal sigma weight residual 93.00 53.91 39.09 1 1.00e+01 1.00e-02 2.15e+01 ... (remaining 20248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.673: 3426 0.673 - 1.346: 0 1.346 - 2.019: 0 2.019 - 2.692: 0 2.692 - 3.365: 1 Chirality restraints: 3427 Sorted by residual: chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 76 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 0.97 -3.37 2.00e-01 2.50e+01 2.83e+02 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 MAN I 6 " pdb=" O6 MAN I 4 " pdb=" C2 MAN I 6 " pdb=" O5 MAN I 6 " both_signs ideal model delta sigma weight residual False 2.40 2.23 0.17 2.00e-02 2.50e+03 7.56e+01 ... (remaining 3424 not shown) Planarity restraints: 5865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 141 " -0.264 2.00e-02 2.50e+03 3.32e-01 1.66e+03 pdb=" CG ASN E 141 " -0.090 2.00e-02 2.50e+03 pdb=" OD1 ASN E 141 " 0.351 2.00e-02 2.50e+03 pdb=" ND2 ASN E 141 " -0.226 2.00e-02 2.50e+03 pdb="HD21 ASN E 141 " 0.552 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " -0.324 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 141 " -0.250 2.00e-02 2.50e+03 3.26e-01 1.59e+03 pdb=" CG ASN B 141 " -0.092 2.00e-02 2.50e+03 pdb=" OD1 ASN B 141 " 0.345 2.00e-02 2.50e+03 pdb=" ND2 ASN B 141 " -0.235 2.00e-02 2.50e+03 pdb="HD21 ASN B 141 " 0.543 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " -0.310 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 143 " -0.249 2.00e-02 2.50e+03 3.25e-01 1.58e+03 pdb=" CG ASN D 143 " -0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN D 143 " 0.344 2.00e-02 2.50e+03 pdb=" ND2 ASN D 143 " -0.237 2.00e-02 2.50e+03 pdb="HD21 ASN D 143 " 0.541 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " -0.309 2.00e-02 2.50e+03 ... (remaining 5862 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 364 2.04 - 2.68: 57915 2.68 - 3.32: 117328 3.32 - 3.96: 160433 3.96 - 4.60: 243206 Nonbonded interactions: 579246 Sorted by model distance: nonbonded pdb=" HE1 TYR B 242 " pdb="HD22 ASN B 301 " model vdw 1.400 2.100 nonbonded pdb=" HH TYR E 15 " pdb=" H TRP E 86 " model vdw 1.430 2.100 nonbonded pdb=" H PHE F 151 " pdb=" HH TYR G 56 " model vdw 1.460 2.100 nonbonded pdb="HD22 ASN B 301 " pdb=" HB3 CYS B 438 " model vdw 1.515 2.270 nonbonded pdb=" HZ1 LYS A 145 " pdb=" HH TYR A 190 " model vdw 1.516 2.100 ... (remaining 579241 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 1 through 127 or (resid 128 and (name N or name CA or name \ C or name O or name CB or name SG or name H or name HA or name HB2 or name HB3) \ ) or resid 129 through 141 or (resid 142 and (name N or name CA or name C or nam \ e O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or resi \ d 143 through 436)) selection = (chain 'C' and (resid 1 through 330 or resid 369 through 436)) } ncs_group { reference = chain 'H' selection = chain 'N' } ncs_group { reference = (chain 'I' and (resid 2 or resid 5 through 7)) selection = (chain 'J' and (resid 1 or resid 4 through 6)) selection = (chain 'L' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain 'K' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.210 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 36.970 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 : 0.006 0.152 21203 Z= 0.308 Angle : 0.869 16.580 28985 Z= 0.442 Chirality : 0.078 3.365 3427 Planarity : 0.015 0.463 3527 Dihedral : 16.511 169.854 8562 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 0.18 % Allowed : 7.29 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.21 (0.17), residues: 2459 helix: 2.24 (0.18), residues: 805 sheet: 0.24 (0.20), residues: 631 loop : 0.11 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 182 TYR 0.022 0.002 TYR G 194 PHE 0.020 0.002 PHE E 267 TRP 0.016 0.001 TRP B 55 HIS 0.013 0.001 HIS G 219 Details of bonding type rmsd covalent geometry : bond 0.00552 (21160) covalent geometry : angle 0.83110 (28865) SS BOND : bond 0.01418 ( 9) SS BOND : angle 1.78711 ( 18) hydrogen bonds : bond 0.11888 ( 999) hydrogen bonds : angle 5.62521 ( 3066) link_ALPHA1-3 : bond 0.00583 ( 8) link_ALPHA1-3 : angle 2.17976 ( 24) link_ALPHA1-6 : bond 0.00296 ( 6) link_ALPHA1-6 : angle 1.54054 ( 18) link_BETA1-4 : bond 0.00711 ( 12) link_BETA1-4 : angle 2.29444 ( 36) link_NAG-ASN : bond 0.13498 ( 8) link_NAG-ASN : angle 7.98925 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 249 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 329 MET cc_start: 0.5378 (ttt) cc_final: 0.4263 (mpt) REVERT: C 391 GLU cc_start: 0.6606 (mt-10) cc_final: 0.6255 (tm-30) REVERT: E 289 LEU cc_start: 0.8354 (tp) cc_final: 0.8097 (mm) REVERT: E 318 GLN cc_start: 0.7551 (mm-40) cc_final: 0.7143 (mm110) REVERT: E 434 LYS cc_start: 0.8204 (tttt) cc_final: 0.7954 (tttp) REVERT: D 222 ARG cc_start: 0.8574 (ttt180) cc_final: 0.8313 (ttp80) REVERT: B 437 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7841 (tp) outliers start: 4 outliers final: 1 residues processed: 250 average time/residue: 1.2705 time to fit residues: 361.4208 Evaluate side-chains 229 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 227 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain G residue 53 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS A 297 ASN A 393 ASN C 186 HIS D 70 ASN B 301 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 GLN F 250 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.152057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.105262 restraints weight = 58629.326| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.68 r_work: 0.3190 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21203 Z= 0.120 Angle : 0.579 10.088 28985 Z= 0.283 Chirality : 0.045 0.653 3427 Planarity : 0.005 0.088 3527 Dihedral : 12.014 169.141 3882 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.63 % Favored : 98.33 % Rotamer: Outliers : 1.02 % Allowed : 7.56 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.45 (0.17), residues: 2459 helix: 2.50 (0.18), residues: 807 sheet: 0.33 (0.20), residues: 646 loop : 0.23 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 480 TYR 0.011 0.001 TYR G 161 PHE 0.015 0.001 PHE E 267 TRP 0.009 0.001 TRP D 62 HIS 0.006 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00255 (21160) covalent geometry : angle 0.56516 (28865) SS BOND : bond 0.00544 ( 9) SS BOND : angle 1.10196 ( 18) hydrogen bonds : bond 0.04865 ( 999) hydrogen bonds : angle 4.61669 ( 3066) link_ALPHA1-3 : bond 0.00638 ( 8) link_ALPHA1-3 : angle 2.11796 ( 24) link_ALPHA1-6 : bond 0.00565 ( 6) link_ALPHA1-6 : angle 1.73659 ( 18) link_BETA1-4 : bond 0.00481 ( 12) link_BETA1-4 : angle 1.92408 ( 36) link_NAG-ASN : bond 0.00582 ( 8) link_NAG-ASN : angle 2.86428 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 237 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 329 MET cc_start: 0.5513 (ttt) cc_final: 0.4556 (mpt) REVERT: C 391 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6154 (tm-30) REVERT: C 407 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7789 (t0) REVERT: E 289 LEU cc_start: 0.8079 (tp) cc_final: 0.7871 (mm) REVERT: E 318 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7086 (mm110) REVERT: E 427 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.5621 (tm-30) REVERT: E 434 LYS cc_start: 0.8175 (tttt) cc_final: 0.7851 (tttp) REVERT: D 222 ARG cc_start: 0.8656 (ttt180) cc_final: 0.8084 (ttp80) REVERT: B 221 LEU cc_start: 0.7632 (tm) cc_final: 0.7297 (tm) REVERT: B 225 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7983 (pt) REVERT: B 437 ILE cc_start: 0.7975 (mt) cc_final: 0.7722 (tp) outliers start: 23 outliers final: 8 residues processed: 246 average time/residue: 1.2110 time to fit residues: 340.3554 Evaluate side-chains 243 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 232 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 1 SER Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain G residue 53 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 137 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 239 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 HIS A 393 ASN ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 HIS G 187 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.149480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102170 restraints weight = 58100.085| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.68 r_work: 0.3142 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21203 Z= 0.166 Angle : 0.584 7.371 28985 Z= 0.296 Chirality : 0.045 0.630 3427 Planarity : 0.005 0.062 3527 Dihedral : 10.612 131.526 3880 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.11 % Favored : 97.84 % Rotamer: Outliers : 1.33 % Allowed : 7.69 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.47 (0.17), residues: 2459 helix: 2.50 (0.17), residues: 807 sheet: 0.45 (0.20), residues: 640 loop : 0.15 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 30 TYR 0.012 0.002 TYR A 72 PHE 0.020 0.002 PHE C 105 TRP 0.012 0.001 TRP D 176 HIS 0.009 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00370 (21160) covalent geometry : angle 0.56943 (28865) SS BOND : bond 0.00674 ( 9) SS BOND : angle 1.35396 ( 18) hydrogen bonds : bond 0.05275 ( 999) hydrogen bonds : angle 4.59647 ( 3066) link_ALPHA1-3 : bond 0.00665 ( 8) link_ALPHA1-3 : angle 1.68056 ( 24) link_ALPHA1-6 : bond 0.00498 ( 6) link_ALPHA1-6 : angle 1.76299 ( 18) link_BETA1-4 : bond 0.00462 ( 12) link_BETA1-4 : angle 2.10247 ( 36) link_NAG-ASN : bond 0.00446 ( 8) link_NAG-ASN : angle 2.84451 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 387 LYS cc_start: 0.7418 (tppt) cc_final: 0.7031 (mmmt) REVERT: C 391 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6309 (tm-30) REVERT: C 407 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7762 (t0) REVERT: E 289 LEU cc_start: 0.8125 (tp) cc_final: 0.7808 (mm) REVERT: E 318 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7098 (mm110) REVERT: E 427 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.5726 (tm-30) REVERT: E 434 LYS cc_start: 0.8238 (tttt) cc_final: 0.7927 (ttmp) REVERT: D 222 ARG cc_start: 0.8674 (ttt180) cc_final: 0.8120 (ttp80) REVERT: B 221 LEU cc_start: 0.7648 (tm) cc_final: 0.7337 (tm) REVERT: B 422 GLU cc_start: 0.6064 (OUTLIER) cc_final: 0.5701 (tm-30) REVERT: B 461 ARG cc_start: 0.7234 (mtt90) cc_final: 0.6552 (mtt90) outliers start: 30 outliers final: 16 residues processed: 250 average time/residue: 1.3308 time to fit residues: 376.5132 Evaluate side-chains 251 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 1 SER Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain G residue 53 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 204 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 243 optimal weight: 9.9990 chunk 171 optimal weight: 0.6980 chunk 150 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 HIS ** B 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.149421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102289 restraints weight = 58117.681| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.68 r_work: 0.3145 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21203 Z= 0.152 Angle : 0.554 5.921 28985 Z= 0.281 Chirality : 0.044 0.461 3427 Planarity : 0.004 0.047 3527 Dihedral : 9.828 118.422 3880 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.79 % Favored : 98.17 % Rotamer: Outliers : 1.47 % Allowed : 7.47 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.51 (0.17), residues: 2459 helix: 2.55 (0.17), residues: 807 sheet: 0.51 (0.20), residues: 634 loop : 0.14 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 30 TYR 0.010 0.001 TYR B 134 PHE 0.018 0.002 PHE E 267 TRP 0.010 0.001 TRP D 176 HIS 0.007 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00335 (21160) covalent geometry : angle 0.54100 (28865) SS BOND : bond 0.00628 ( 9) SS BOND : angle 1.24930 ( 18) hydrogen bonds : bond 0.05043 ( 999) hydrogen bonds : angle 4.48002 ( 3066) link_ALPHA1-3 : bond 0.00708 ( 8) link_ALPHA1-3 : angle 1.80535 ( 24) link_ALPHA1-6 : bond 0.00710 ( 6) link_ALPHA1-6 : angle 1.72405 ( 18) link_BETA1-4 : bond 0.00404 ( 12) link_BETA1-4 : angle 2.07229 ( 36) link_NAG-ASN : bond 0.00292 ( 8) link_NAG-ASN : angle 2.31431 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 387 LYS cc_start: 0.7259 (tppt) cc_final: 0.7005 (mmmt) REVERT: C 391 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6323 (tm-30) REVERT: C 407 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7738 (t0) REVERT: E 2 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: E 318 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7124 (mm110) REVERT: E 427 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.5747 (tm-30) REVERT: E 434 LYS cc_start: 0.8266 (tttt) cc_final: 0.7988 (ttmp) REVERT: D 222 ARG cc_start: 0.8663 (ttt180) cc_final: 0.8107 (ttp80) REVERT: B 83 GLU cc_start: 0.7930 (mp0) cc_final: 0.7717 (mp0) REVERT: B 221 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7328 (tp) REVERT: B 247 GLN cc_start: 0.7382 (mt0) cc_final: 0.7049 (mp10) REVERT: B 461 ARG cc_start: 0.7231 (mtt90) cc_final: 0.6558 (mtt90) REVERT: G 99 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7277 (mm-30) outliers start: 33 outliers final: 15 residues processed: 251 average time/residue: 1.4949 time to fit residues: 425.0853 Evaluate side-chains 253 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 234 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 1 SER Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain G residue 53 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 154 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN C 408 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.149605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102453 restraints weight = 58101.601| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.72 r_work: 0.3147 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21203 Z= 0.137 Angle : 0.540 6.194 28985 Z= 0.274 Chirality : 0.044 0.425 3427 Planarity : 0.004 0.045 3527 Dihedral : 9.200 108.918 3880 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.95 % Favored : 98.01 % Rotamer: Outliers : 1.51 % Allowed : 7.91 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.59 (0.17), residues: 2459 helix: 2.63 (0.17), residues: 808 sheet: 0.52 (0.20), residues: 634 loop : 0.18 (0.20), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 30 TYR 0.010 0.001 TYR B 134 PHE 0.017 0.002 PHE C 284 TRP 0.009 0.001 TRP D 176 HIS 0.006 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00301 (21160) covalent geometry : angle 0.52726 (28865) SS BOND : bond 0.00568 ( 9) SS BOND : angle 1.11791 ( 18) hydrogen bonds : bond 0.04863 ( 999) hydrogen bonds : angle 4.40477 ( 3066) link_ALPHA1-3 : bond 0.00687 ( 8) link_ALPHA1-3 : angle 1.69688 ( 24) link_ALPHA1-6 : bond 0.00971 ( 6) link_ALPHA1-6 : angle 2.28151 ( 18) link_BETA1-4 : bond 0.00352 ( 12) link_BETA1-4 : angle 1.99791 ( 36) link_NAG-ASN : bond 0.00286 ( 8) link_NAG-ASN : angle 2.14512 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 391 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6307 (tm-30) REVERT: C 407 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7809 (t0) REVERT: C 420 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.6959 (mm) REVERT: E 2 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7700 (mt-10) REVERT: E 289 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7791 (mm) REVERT: E 318 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7114 (mm110) REVERT: E 427 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.5662 (tm-30) REVERT: E 434 LYS cc_start: 0.8262 (tttt) cc_final: 0.7973 (tttp) REVERT: D 222 ARG cc_start: 0.8661 (ttt180) cc_final: 0.8137 (ttp80) REVERT: B 221 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7287 (tp) REVERT: B 247 GLN cc_start: 0.7348 (mt0) cc_final: 0.7029 (mp10) REVERT: B 461 ARG cc_start: 0.7226 (mtt90) cc_final: 0.6583 (mtt90) REVERT: G 99 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7272 (mm-30) outliers start: 34 outliers final: 18 residues processed: 254 average time/residue: 1.3576 time to fit residues: 391.2731 Evaluate side-chains 262 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain E residue 1 SER Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 127 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 193 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 243 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN ** A 408 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.147805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.100416 restraints weight = 58070.962| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.68 r_work: 0.3118 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 21203 Z= 0.224 Angle : 0.618 6.275 28985 Z= 0.317 Chirality : 0.046 0.441 3427 Planarity : 0.005 0.051 3527 Dihedral : 9.585 97.415 3880 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.07 % Favored : 97.89 % Rotamer: Outliers : 1.38 % Allowed : 8.00 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.40 (0.17), residues: 2459 helix: 2.43 (0.17), residues: 809 sheet: 0.46 (0.20), residues: 641 loop : 0.09 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 30 TYR 0.016 0.002 TYR B 179 PHE 0.023 0.002 PHE C 105 TRP 0.015 0.002 TRP D 176 HIS 0.007 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00510 (21160) covalent geometry : angle 0.60273 (28865) SS BOND : bond 0.00879 ( 9) SS BOND : angle 1.57788 ( 18) hydrogen bonds : bond 0.05668 ( 999) hydrogen bonds : angle 4.62811 ( 3066) link_ALPHA1-3 : bond 0.00676 ( 8) link_ALPHA1-3 : angle 1.75517 ( 24) link_ALPHA1-6 : bond 0.00954 ( 6) link_ALPHA1-6 : angle 2.37596 ( 18) link_BETA1-4 : bond 0.00554 ( 12) link_BETA1-4 : angle 2.27334 ( 36) link_NAG-ASN : bond 0.00561 ( 8) link_NAG-ASN : angle 2.60352 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 LYS cc_start: 0.8940 (mtpp) cc_final: 0.8679 (mttm) REVERT: C 391 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6372 (tm-30) REVERT: C 407 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7709 (t0) REVERT: C 420 ILE cc_start: 0.7212 (OUTLIER) cc_final: 0.6896 (mm) REVERT: E 2 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: E 30 ARG cc_start: 0.8575 (mtp85) cc_final: 0.8375 (mtp85) REVERT: E 289 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7908 (mm) REVERT: E 318 GLN cc_start: 0.7516 (mm-40) cc_final: 0.7015 (mm110) REVERT: E 427 GLN cc_start: 0.7208 (OUTLIER) cc_final: 0.5792 (tm-30) REVERT: E 434 LYS cc_start: 0.8275 (tttt) cc_final: 0.7970 (tttp) REVERT: D 222 ARG cc_start: 0.8685 (ttt180) cc_final: 0.8112 (ttp80) REVERT: B 247 GLN cc_start: 0.7346 (mt0) cc_final: 0.7037 (mp10) REVERT: B 461 ARG cc_start: 0.7201 (mtt90) cc_final: 0.6549 (mtt90) REVERT: G 99 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7271 (mm-30) REVERT: G 101 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7732 (pm20) REVERT: G 189 SER cc_start: 0.7956 (t) cc_final: 0.7694 (p) outliers start: 31 outliers final: 18 residues processed: 249 average time/residue: 1.4311 time to fit residues: 403.6497 Evaluate side-chains 258 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 234 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain E residue 1 SER Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 127 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 242 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN C 408 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.148177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.100959 restraints weight = 58094.285| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.68 r_work: 0.3127 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21203 Z= 0.188 Angle : 0.588 6.445 28985 Z= 0.301 Chirality : 0.045 0.415 3427 Planarity : 0.005 0.043 3527 Dihedral : 9.437 86.411 3880 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Rotamer: Outliers : 1.51 % Allowed : 8.14 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.39 (0.17), residues: 2459 helix: 2.42 (0.17), residues: 810 sheet: 0.44 (0.20), residues: 639 loop : 0.09 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 313 TYR 0.012 0.002 TYR B 179 PHE 0.019 0.002 PHE C 284 TRP 0.012 0.002 TRP D 176 HIS 0.007 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00422 (21160) covalent geometry : angle 0.57408 (28865) SS BOND : bond 0.00771 ( 9) SS BOND : angle 1.41886 ( 18) hydrogen bonds : bond 0.05402 ( 999) hydrogen bonds : angle 4.56069 ( 3066) link_ALPHA1-3 : bond 0.00667 ( 8) link_ALPHA1-3 : angle 1.69080 ( 24) link_ALPHA1-6 : bond 0.00880 ( 6) link_ALPHA1-6 : angle 2.45206 ( 18) link_BETA1-4 : bond 0.00475 ( 12) link_BETA1-4 : angle 2.13682 ( 36) link_NAG-ASN : bond 0.00422 ( 8) link_NAG-ASN : angle 2.36303 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.6915 (OUTLIER) cc_final: 0.6704 (m-30) REVERT: C 2 GLU cc_start: 0.6515 (pm20) cc_final: 0.6248 (tm-30) REVERT: C 76 LYS cc_start: 0.8931 (mtpp) cc_final: 0.8675 (mttm) REVERT: C 391 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6387 (tm-30) REVERT: C 407 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7752 (t0) REVERT: C 420 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6936 (mm) REVERT: E 2 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: E 289 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7870 (mm) REVERT: E 318 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7060 (mm110) REVERT: E 427 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.5782 (tm-30) REVERT: E 434 LYS cc_start: 0.8295 (tttt) cc_final: 0.7998 (tttp) REVERT: D 222 ARG cc_start: 0.8641 (ttt180) cc_final: 0.8084 (ttp80) REVERT: D 437 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7695 (tp30) REVERT: B 247 GLN cc_start: 0.7399 (mt0) cc_final: 0.7097 (mp10) REVERT: B 426 ASP cc_start: 0.6305 (m-30) cc_final: 0.5991 (m-30) REVERT: G 99 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7214 (mm-30) REVERT: G 188 ASP cc_start: 0.7486 (t70) cc_final: 0.7174 (t70) REVERT: G 189 SER cc_start: 0.8036 (t) cc_final: 0.7496 (p) outliers start: 34 outliers final: 16 residues processed: 255 average time/residue: 1.4621 time to fit residues: 421.3125 Evaluate side-chains 255 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 232 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain E residue 1 SER Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 427 GLN Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 127 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 223 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 chunk 181 optimal weight: 0.0870 chunk 73 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 208 optimal weight: 0.2980 chunk 241 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN C 217 ASN C 408 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.150523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103881 restraints weight = 58271.097| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.68 r_work: 0.3170 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21203 Z= 0.104 Angle : 0.512 6.032 28985 Z= 0.260 Chirality : 0.043 0.317 3427 Planarity : 0.004 0.056 3527 Dihedral : 8.587 85.400 3880 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.55 % Favored : 98.41 % Rotamer: Outliers : 1.11 % Allowed : 8.58 % Favored : 90.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.66 (0.17), residues: 2459 helix: 2.76 (0.17), residues: 810 sheet: 0.47 (0.20), residues: 634 loop : 0.23 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 30 TYR 0.010 0.001 TYR F 125 PHE 0.015 0.001 PHE C 284 TRP 0.011 0.001 TRP D 62 HIS 0.003 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00222 (21160) covalent geometry : angle 0.50081 (28865) SS BOND : bond 0.00405 ( 9) SS BOND : angle 0.84120 ( 18) hydrogen bonds : bond 0.04437 ( 999) hydrogen bonds : angle 4.26854 ( 3066) link_ALPHA1-3 : bond 0.00752 ( 8) link_ALPHA1-3 : angle 1.68601 ( 24) link_ALPHA1-6 : bond 0.00873 ( 6) link_ALPHA1-6 : angle 2.19112 ( 18) link_BETA1-4 : bond 0.00327 ( 12) link_BETA1-4 : angle 1.79675 ( 36) link_NAG-ASN : bond 0.00175 ( 8) link_NAG-ASN : angle 1.79191 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8671 (mttm) REVERT: C 391 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6333 (tm-30) REVERT: C 407 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7784 (t0) REVERT: C 415 MET cc_start: 0.8342 (mmt) cc_final: 0.7932 (mmt) REVERT: E 2 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7644 (mt-10) REVERT: E 209 ARG cc_start: 0.8523 (mtt90) cc_final: 0.8253 (mtt90) REVERT: E 225 TYR cc_start: 0.8583 (m-80) cc_final: 0.8337 (m-80) REVERT: E 289 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7942 (mm) REVERT: E 318 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7059 (mm110) REVERT: E 434 LYS cc_start: 0.8258 (tttt) cc_final: 0.7976 (tttp) REVERT: D 222 ARG cc_start: 0.8641 (ttt180) cc_final: 0.8149 (ttp80) REVERT: B 247 GLN cc_start: 0.7334 (mt0) cc_final: 0.7027 (mp10) REVERT: G 101 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7729 (pm20) REVERT: G 188 ASP cc_start: 0.7414 (t70) cc_final: 0.7151 (t70) REVERT: G 189 SER cc_start: 0.7970 (t) cc_final: 0.7425 (p) outliers start: 25 outliers final: 12 residues processed: 256 average time/residue: 1.3866 time to fit residues: 403.0643 Evaluate side-chains 258 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 242 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain E residue 1 SER Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 127 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 54 optimal weight: 0.1980 chunk 190 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN C 408 HIS B 301 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.149971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103152 restraints weight = 58383.269| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.67 r_work: 0.3159 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21203 Z= 0.124 Angle : 0.526 6.874 28985 Z= 0.266 Chirality : 0.043 0.298 3427 Planarity : 0.004 0.053 3527 Dihedral : 8.534 86.448 3880 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.83 % Favored : 98.13 % Rotamer: Outliers : 0.93 % Allowed : 8.94 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.72 (0.17), residues: 2459 helix: 2.80 (0.17), residues: 809 sheet: 0.51 (0.20), residues: 635 loop : 0.27 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 313 TYR 0.010 0.001 TYR A 401 PHE 0.016 0.001 PHE E 267 TRP 0.008 0.001 TRP D 176 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00274 (21160) covalent geometry : angle 0.51398 (28865) SS BOND : bond 0.00560 ( 9) SS BOND : angle 1.11871 ( 18) hydrogen bonds : bond 0.04615 ( 999) hydrogen bonds : angle 4.28063 ( 3066) link_ALPHA1-3 : bond 0.00696 ( 8) link_ALPHA1-3 : angle 1.73121 ( 24) link_ALPHA1-6 : bond 0.00868 ( 6) link_ALPHA1-6 : angle 2.14070 ( 18) link_BETA1-4 : bond 0.00353 ( 12) link_BETA1-4 : angle 1.85883 ( 36) link_NAG-ASN : bond 0.00262 ( 8) link_NAG-ASN : angle 1.87626 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 391 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6376 (tm-30) REVERT: C 407 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7742 (t0) REVERT: C 415 MET cc_start: 0.8315 (mmt) cc_final: 0.7911 (mmt) REVERT: C 420 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.7020 (mm) REVERT: E 2 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7709 (mt-10) REVERT: E 225 TYR cc_start: 0.8596 (m-80) cc_final: 0.8348 (m-80) REVERT: E 289 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7934 (mm) REVERT: E 318 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7043 (mm110) REVERT: E 434 LYS cc_start: 0.8264 (tttt) cc_final: 0.7980 (tttp) REVERT: D 222 ARG cc_start: 0.8659 (ttt180) cc_final: 0.8166 (ttp80) REVERT: B 247 GLN cc_start: 0.7395 (mt0) cc_final: 0.7046 (mp10) REVERT: B 461 ARG cc_start: 0.7157 (mtt90) cc_final: 0.6659 (mtt90) REVERT: G 101 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7736 (pm20) REVERT: G 188 ASP cc_start: 0.7360 (t70) cc_final: 0.7125 (t70) REVERT: G 189 SER cc_start: 0.7971 (t) cc_final: 0.7440 (p) outliers start: 21 outliers final: 13 residues processed: 250 average time/residue: 1.2881 time to fit residues: 364.3785 Evaluate side-chains 256 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 238 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain E residue 1 SER Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain B residue 435 ASP Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 127 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 150 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 178 optimal weight: 0.5980 chunk 161 optimal weight: 0.9990 chunk 4 optimal weight: 0.0470 chunk 115 optimal weight: 0.9980 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN C 408 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.151150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.104584 restraints weight = 58112.877| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.68 r_work: 0.3182 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 21203 Z= 0.101 Angle : 0.502 9.477 28985 Z= 0.254 Chirality : 0.042 0.265 3427 Planarity : 0.004 0.056 3527 Dihedral : 8.182 85.214 3880 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.67 % Favored : 98.29 % Rotamer: Outliers : 0.84 % Allowed : 8.98 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.80 (0.17), residues: 2459 helix: 2.94 (0.18), residues: 803 sheet: 0.51 (0.20), residues: 638 loop : 0.31 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 313 TYR 0.010 0.001 TYR A 401 PHE 0.017 0.001 PHE C 280 TRP 0.010 0.001 TRP D 62 HIS 0.003 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00219 (21160) covalent geometry : angle 0.49241 (28865) SS BOND : bond 0.00390 ( 9) SS BOND : angle 0.76632 ( 18) hydrogen bonds : bond 0.04244 ( 999) hydrogen bonds : angle 4.16610 ( 3066) link_ALPHA1-3 : bond 0.00696 ( 8) link_ALPHA1-3 : angle 1.69554 ( 24) link_ALPHA1-6 : bond 0.00890 ( 6) link_ALPHA1-6 : angle 2.00237 ( 18) link_BETA1-4 : bond 0.00327 ( 12) link_BETA1-4 : angle 1.70179 ( 36) link_NAG-ASN : bond 0.00157 ( 8) link_NAG-ASN : angle 1.60987 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4918 Ramachandran restraints generated. 2459 Oldfield, 0 Emsley, 2459 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 245 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2 GLU cc_start: 0.6434 (pm20) cc_final: 0.5874 (pm20) REVERT: C 391 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6283 (tm-30) REVERT: C 407 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7716 (t0) REVERT: C 415 MET cc_start: 0.8268 (mmt) cc_final: 0.7940 (mmt) REVERT: C 420 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7119 (mm) REVERT: E 2 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: E 209 ARG cc_start: 0.8493 (mtt90) cc_final: 0.8219 (mtt90) REVERT: E 225 TYR cc_start: 0.8565 (m-80) cc_final: 0.8244 (m-80) REVERT: E 289 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7952 (mm) REVERT: E 318 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7043 (mm110) REVERT: E 434 LYS cc_start: 0.8230 (tttt) cc_final: 0.7945 (tttp) REVERT: D 222 ARG cc_start: 0.8632 (ttt180) cc_final: 0.8148 (ttp80) REVERT: D 436 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6890 (mm-30) REVERT: B 247 GLN cc_start: 0.7357 (mt0) cc_final: 0.6964 (mp10) REVERT: B 461 ARG cc_start: 0.7156 (mtt90) cc_final: 0.6657 (mtt90) REVERT: G 99 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7211 (mm-30) REVERT: G 101 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7738 (pm20) REVERT: G 189 SER cc_start: 0.7964 (t) cc_final: 0.7445 (p) outliers start: 19 outliers final: 11 residues processed: 251 average time/residue: 1.3003 time to fit residues: 371.3936 Evaluate side-chains 256 residues out of total 2249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 239 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 301 ARG Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain E residue 1 SER Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 127 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 186 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 239 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 393 ASN C 408 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.148146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.100864 restraints weight = 58236.326| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.68 r_work: 0.3125 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21203 Z= 0.208 Angle : 0.603 7.182 28985 Z= 0.308 Chirality : 0.045 0.298 3427 Planarity : 0.005 0.057 3527 Dihedral : 8.819 88.413 3880 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.03 % Favored : 97.93 % Rotamer: Outliers : 0.98 % Allowed : 9.07 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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 aren not related in a simple way. whole: 1.57 (0.17), residues: 2459 helix: 2.61 (0.17), residues: 804 sheet: 0.48 (0.20), residues: 643 loop : 0.22 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 313 TYR 0.016 0.002 TYR B 134 PHE 0.021 0.002 PHE E 267 TRP 0.013 0.002 TRP D 176 HIS 0.007 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00477 (21160) covalent geometry : angle 0.58987 (28865) SS BOND : bond 0.00849 ( 9) SS BOND : angle 1.52245 ( 18) hydrogen bonds : bond 0.05387 ( 999) hydrogen bonds : angle 4.48500 ( 3066) link_ALPHA1-3 : bond 0.00634 ( 8) link_ALPHA1-3 : angle 1.77972 ( 24) link_ALPHA1-6 : bond 0.00852 ( 6) link_ALPHA1-6 : angle 2.27373 ( 18) link_BETA1-4 : bond 0.00520 ( 12) link_BETA1-4 : angle 2.16961 ( 36) link_NAG-ASN : bond 0.00474 ( 8) link_NAG-ASN : angle 2.22261 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20352.23 seconds wall clock time: 343 minutes 31.95 seconds (20611.95 seconds total)