Starting phenix.real_space_refine on Thu Mar 5 20:56:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m17_30039/03_2026/6m17_30039.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m17_30039/03_2026/6m17_30039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6m17_30039/03_2026/6m17_30039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m17_30039/03_2026/6m17_30039.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m17_30039/03_2026/6m17_30039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m17_30039/03_2026/6m17_30039.map" } resolution = 2.9 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 ------------------------------------------------------------------------------- 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= 0.006 sd= 0.100 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 142 5.16 5 C 16396 2.51 5 N 4054 2.21 5 O 4750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25344 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} Chain: "B" Number of atoms: 6089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6089 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 35, 'TRANS': 712} Chain: "E" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1462 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "C" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} Chain: "D" Number of atoms: 6089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6089 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 35, 'TRANS': 712} Chain: "F" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1462 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 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: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {'NAG': 4} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 5.72, per 1000 atoms: 0.23 Number of scatterers: 25344 At special positions: 0 Unit cell: (114.135, 148.919, 214.139, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 142 16.00 O 4750 8.00 N 4054 7.00 C 16396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.66 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.17 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.54 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.37 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 383 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.66 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.17 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.54 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.04 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.37 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " NAG N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " NAG V 3 " NAG-ASN " NAG A 701 " - " ASN A 158 " " NAG A 702 " - " ASN A 182 " " NAG A 703 " - " ASN A 354 " " NAG A 704 " - " ASN A 368 " " NAG B 901 " - " ASN B 322 " " NAG C 701 " - " ASN C 158 " " NAG C 702 " - " ASN C 182 " " NAG C 703 " - " ASN C 354 " " NAG C 704 " - " ASN C 368 " " NAG D 901 " - " ASN D 322 " " NAG G 1 " - " ASN A 258 " " NAG H 1 " - " ASN B 53 " " NAG I 1 " - " ASN B 90 " " NAG J 1 " - " ASN B 103 " " NAG K 1 " - " ASN B 432 " " NAG L 1 " - " ASN B 546 " " NAG M 1 " - " ASN B 690 " " NAG N 1 " - " ASN E 343 " " NAG O 1 " - " ASN C 258 " " NAG P 1 " - " ASN D 53 " " NAG Q 1 " - " ASN D 90 " " NAG R 1 " - " ASN D 103 " " NAG S 1 " - " ASN D 432 " " NAG T 1 " - " ASN D 546 " " NAG U 1 " - " ASN D 690 " " NAG V 1 " - " ASN F 343 " Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 902 " pdb="ZN ZN B 902 " - pdb=" NE2 HIS B 374 " pdb=" ZN D 902 " pdb="ZN ZN D 902 " - pdb=" NE2 HIS D 374 " 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5760 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 14 sheets defined 59.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 37 through 49 removed outlier: 3.860A pdb=" N TYR A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 4.244A pdb=" N SER A 64 " --> pdb=" O TYR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 81 Processing helix chain 'A' and resid 81 through 97 removed outlier: 3.651A pdb=" N ALA A 91 " --> pdb=" O TYR A 87 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 removed outlier: 3.721A pdb=" N TRP A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 142 removed outlier: 3.551A pdb=" N SER A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 133 " --> pdb=" O TYR A 129 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 134 " --> pdb=" O ASN A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 169 removed outlier: 3.589A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.977A pdb=" N CYS A 200 " --> pdb=" O TRP A 196 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 242 removed outlier: 3.733A pdb=" N ALA A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR A 228 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix removed outlier: 3.728A pdb=" N THR A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 Processing helix chain 'A' and resid 258 through 264 removed outlier: 3.629A pdb=" N GLN A 264 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.528A pdb=" N ASP A 270 " --> pdb=" O ASP A 266 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 291 removed outlier: 3.838A pdb=" N SER A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 317 removed outlier: 3.625A pdb=" N SER A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 346 removed outlier: 3.771A pdb=" N SER A 323 " --> pdb=" O ILE A 319 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 344 " --> pdb=" O ASN A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 371 removed outlier: 4.406A pdb=" N GLN A 365 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 removed outlier: 4.014A pdb=" N THR A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 3.511A pdb=" N VAL A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 420 " --> pdb=" O TRP A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 445 removed outlier: 4.267A pdb=" N GLY A 434 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A 435 " --> pdb=" O SER A 431 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A 437 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 454 through 470 removed outlier: 4.023A pdb=" N LEU A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 474 Processing helix chain 'A' and resid 477 through 507 removed outlier: 3.640A pdb=" N LEU A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) Proline residue: A 493 - end of helix removed outlier: 3.783A pdb=" N ILE A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 497 " --> pdb=" O PRO A 493 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 522 removed outlier: 3.873A pdb=" N LYS A 516 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 removed outlier: 3.596A pdb=" N THR A 533 " --> pdb=" O PHE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 546 removed outlier: 3.767A pdb=" N LEU A 540 " --> pdb=" O VAL A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 554 removed outlier: 4.202A pdb=" N PHE A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 554 " --> pdb=" O PHE A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 609 removed outlier: 3.879A pdb=" N VAL A 585 " --> pdb=" O TRP A 581 " (cutoff:3.500A) Proline residue: A 593 - end of helix removed outlier: 3.837A pdb=" N ILE A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Proline residue: A 598 - end of helix Processing helix chain 'B' and resid 22 through 53 removed outlier: 3.814A pdb=" N LYS B 31 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU B 37 " --> pdb=" O ASN B 33 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 81 removed outlier: 3.756A pdb=" N ASN B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 102 removed outlier: 3.640A pdb=" N GLN B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 129 removed outlier: 3.688A pdb=" N LYS B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 155 removed outlier: 3.528A pdb=" N ILE B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 193 removed outlier: 3.608A pdb=" N TRP B 168 " --> pdb=" O ALA B 164 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 3.883A pdb=" N VAL B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 Processing helix chain 'B' and resid 205 through 208 removed outlier: 3.565A pdb=" N GLU B 208 " --> pdb=" O GLY B 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 220 through 231 removed outlier: 3.907A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU B 231 " --> pdb=" O GLU B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.595A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.513A pdb=" N VAL B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 319 removed outlier: 4.309A pdb=" N ILE B 307 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.759A pdb=" N SER B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 383 removed outlier: 3.636A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 removed outlier: 3.548A pdb=" N ARG B 393 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 413 removed outlier: 3.552A pdb=" N ALA B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 405 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 411 " --> pdb=" O ILE B 407 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 412 " --> pdb=" O MET B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 removed outlier: 3.679A pdb=" N SER B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 444 removed outlier: 3.597A pdb=" N GLU B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 436 " --> pdb=" O ASN B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 465 Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.751A pdb=" N TRP B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 482 " --> pdb=" O TRP B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 502 removed outlier: 3.593A pdb=" N SER B 502 " --> pdb=" O ASP B 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 499 through 502' Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 533 removed outlier: 3.878A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 520 " --> pdb=" O TYR B 516 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 532 " --> pdb=" O ALA B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 548 through 559 removed outlier: 4.396A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 572 removed outlier: 3.675A pdb=" N GLU B 571 " --> pdb=" O THR B 567 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 588 removed outlier: 3.577A pdb=" N TYR B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 599 removed outlier: 3.576A pdb=" N TRP B 594 " --> pdb=" O PRO B 590 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP B 597 " --> pdb=" O THR B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 628 removed outlier: 3.643A pdb=" N ALA B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 658 removed outlier: 3.606A pdb=" N MET B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.502A pdb=" N SER B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 716 removed outlier: 3.570A pdb=" N ASP B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 715 " --> pdb=" O ILE B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 766 removed outlier: 3.933A pdb=" N ILE B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 758 " --> pdb=" O VAL B 754 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 762 " --> pdb=" O VAL B 758 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY B 764 " --> pdb=" O LEU B 760 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 344 Processing helix chain 'E' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE E 410 " --> pdb=" O VAL E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.867A pdb=" N TYR E 421 " --> pdb=" O LYS E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 37 through 49 removed outlier: 3.860A pdb=" N TYR C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 removed outlier: 4.244A pdb=" N SER C 64 " --> pdb=" O TYR C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 81 Processing helix chain 'C' and resid 81 through 97 removed outlier: 3.651A pdb=" N ALA C 91 " --> pdb=" O TYR C 87 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 93 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 96 " --> pdb=" O ILE C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 removed outlier: 3.721A pdb=" N TRP C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 142 removed outlier: 3.551A pdb=" N SER C 122 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL C 125 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 126 " --> pdb=" O SER C 122 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR C 128 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN C 130 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 133 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER C 134 " --> pdb=" O ASN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 169 removed outlier: 3.589A pdb=" N ARG C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 195 through 212 removed outlier: 3.977A pdb=" N CYS C 200 " --> pdb=" O TRP C 196 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 201 " --> pdb=" O MET C 197 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYS C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 242 removed outlier: 3.733A pdb=" N ALA C 222 " --> pdb=" O THR C 218 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR C 228 " --> pdb=" O TYR C 224 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix removed outlier: 3.728A pdb=" N THR C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE C 239 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 256 Processing helix chain 'C' and resid 258 through 264 removed outlier: 3.629A pdb=" N GLN C 264 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 279 removed outlier: 3.528A pdb=" N ASP C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 291 removed outlier: 3.838A pdb=" N SER C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 317 removed outlier: 3.625A pdb=" N SER C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE C 308 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE C 312 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 314 " --> pdb=" O ASN C 310 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 346 removed outlier: 3.771A pdb=" N SER C 323 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 344 " --> pdb=" O ASN C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 371 removed outlier: 4.406A pdb=" N GLN C 365 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN C 368 " --> pdb=" O GLN C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 408 removed outlier: 4.014A pdb=" N THR C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 430 removed outlier: 3.511A pdb=" N VAL C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 420 " --> pdb=" O TRP C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 445 removed outlier: 4.267A pdb=" N GLY C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN C 435 " --> pdb=" O SER C 431 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C 437 " --> pdb=" O PHE C 433 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL C 439 " --> pdb=" O ASN C 435 " (cutoff:3.500A) Proline residue: C 442 - end of helix Processing helix chain 'C' and resid 454 through 470 removed outlier: 4.023A pdb=" N LEU C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY C 460 " --> pdb=" O GLU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 474 Processing helix chain 'C' and resid 477 through 507 removed outlier: 3.640A pdb=" N LEU C 482 " --> pdb=" O GLY C 478 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 484 " --> pdb=" O TYR C 480 " (cutoff:3.500A) Proline residue: C 493 - end of helix removed outlier: 3.783A pdb=" N ILE C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE C 497 " --> pdb=" O PRO C 493 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 522 removed outlier: 3.873A pdb=" N LYS C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C 517 " --> pdb=" O ARG C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 536 removed outlier: 3.596A pdb=" N THR C 533 " --> pdb=" O PHE C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 546 removed outlier: 3.767A pdb=" N LEU C 540 " --> pdb=" O VAL C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 554 removed outlier: 4.202A pdb=" N PHE C 550 " --> pdb=" O PHE C 546 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL C 554 " --> pdb=" O PHE C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 609 removed outlier: 3.879A pdb=" N VAL C 585 " --> pdb=" O TRP C 581 " (cutoff:3.500A) Proline residue: C 593 - end of helix removed outlier: 3.837A pdb=" N ILE C 597 " --> pdb=" O PRO C 593 " (cutoff:3.500A) Proline residue: C 598 - end of helix Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.814A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU D 37 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 81 removed outlier: 3.756A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.640A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.688A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.528A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 193 removed outlier: 3.608A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.883A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 Processing helix chain 'D' and resid 205 through 208 removed outlier: 3.565A pdb=" N GLU D 208 " --> pdb=" O GLY D 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 208' Processing helix chain 'D' and resid 220 through 231 removed outlier: 3.907A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 3.595A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.513A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 4.309A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.759A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.636A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.548A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.552A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 412 " --> pdb=" O MET D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.679A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.597A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.751A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 removed outlier: 3.593A pdb=" N SER D 502 " --> pdb=" O ASP D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 499 through 502' Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.878A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 548 through 559 removed outlier: 4.396A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 559 " --> pdb=" O PHE D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.675A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.577A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.576A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 623 through 628 removed outlier: 3.643A pdb=" N ALA D 627 " --> pdb=" O SER D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 658 removed outlier: 3.606A pdb=" N MET D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 668 No H-bonds generated for 'chain 'D' and resid 666 through 668' Processing helix chain 'D' and resid 696 through 707 removed outlier: 3.502A pdb=" N SER D 707 " --> pdb=" O ALA D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 716 removed outlier: 3.570A pdb=" N ASP D 713 " --> pdb=" O SER D 709 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 715 " --> pdb=" O ILE D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 766 removed outlier: 3.933A pdb=" N ILE D 744 " --> pdb=" O SER D 740 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 758 " --> pdb=" O VAL D 754 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE D 762 " --> pdb=" O VAL D 758 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY D 764 " --> pdb=" O LEU D 760 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 344 Processing helix chain 'F' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN F 388 " --> pdb=" O THR F 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP F 389 " --> pdb=" O LYS F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE F 410 " --> pdb=" O VAL F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 removed outlier: 3.867A pdb=" N TYR F 421 " --> pdb=" O LYS F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 559 through 562 removed outlier: 4.380A pdb=" N GLN A 574 " --> pdb=" O ILE A 562 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 132 through 134 removed outlier: 10.037A pdb=" N VAL B 132 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLN B 139 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN B 134 " --> pdb=" O ASN B 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.029A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 347 through 352 removed outlier: 3.582A pdb=" N LEU B 351 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 670 through 673 Processing sheet with id=AA6, first strand: chain 'E' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR E 449 " --> pdb=" O PHE E 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE E 497 " --> pdb=" O TYR E 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR E 451 " --> pdb=" O TYR E 495 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 559 through 562 removed outlier: 4.380A pdb=" N GLN C 574 " --> pdb=" O ILE C 562 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 132 through 134 removed outlier: 10.037A pdb=" N VAL D 132 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLN D 139 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN D 134 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.029A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.582A pdb=" N LEU D 351 " --> pdb=" O ASP D 355 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 670 through 673 Processing sheet with id=AB4, first strand: chain 'F' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL F 395 " --> pdb=" O ILE F 358 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR F 449 " --> pdb=" O PHE F 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE F 497 " --> pdb=" O TYR F 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR F 451 " --> pdb=" O TYR F 495 " (cutoff:3.500A) 1062 hydrogen bonds defined for protein. 3072 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4822 1.33 - 1.45: 7124 1.45 - 1.58: 13852 1.58 - 1.70: 0 1.70 - 1.82: 224 Bond restraints: 26022 Sorted by residual: bond pdb=" N PRO D 135 " pdb=" CD PRO D 135 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" N PRO B 135 " pdb=" CD PRO B 135 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" N PRO B 677 " pdb=" CD PRO B 677 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.88e+01 bond pdb=" N PRO D 677 " pdb=" CD PRO D 677 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.88e+01 bond pdb=" N PRO C 73 " pdb=" CD PRO C 73 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.80e+01 ... (remaining 26017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 34430 2.69 - 5.38: 846 5.38 - 8.07: 108 8.07 - 10.76: 12 10.76 - 13.45: 18 Bond angle restraints: 35414 Sorted by residual: angle pdb=" N GLU A 157 " pdb=" CA GLU A 157 " pdb=" C GLU A 157 " ideal model delta sigma weight residual 111.03 99.23 11.80 1.11e+00 8.12e-01 1.13e+02 angle pdb=" N GLU C 157 " pdb=" CA GLU C 157 " pdb=" C GLU C 157 " ideal model delta sigma weight residual 111.03 99.23 11.80 1.11e+00 8.12e-01 1.13e+02 angle pdb=" N LEU D 143 " pdb=" CA LEU D 143 " pdb=" C LEU D 143 " ideal model delta sigma weight residual 107.62 120.24 -12.62 1.97e+00 2.58e-01 4.11e+01 angle pdb=" N LEU B 143 " pdb=" CA LEU B 143 " pdb=" C LEU B 143 " ideal model delta sigma weight residual 107.62 120.24 -12.62 1.97e+00 2.58e-01 4.11e+01 angle pdb=" N LEU B 144 " pdb=" CA LEU B 144 " pdb=" C LEU B 144 " ideal model delta sigma weight residual 110.80 124.18 -13.38 2.13e+00 2.20e-01 3.95e+01 ... (remaining 35409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 13920 17.68 - 35.37: 1402 35.37 - 53.05: 366 53.05 - 70.74: 102 70.74 - 88.42: 34 Dihedral angle restraints: 15824 sinusoidal: 6850 harmonic: 8974 Sorted by residual: dihedral pdb=" CA TYR E 421 " pdb=" C TYR E 421 " pdb=" N ASN E 422 " pdb=" CA ASN E 422 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA TYR F 421 " pdb=" C TYR F 421 " pdb=" N ASN F 422 " pdb=" CA ASN F 422 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CB CYS F 336 " pdb=" SG CYS F 336 " pdb=" SG CYS F 361 " pdb=" CB CYS F 361 " ideal model delta sinusoidal sigma weight residual -86.00 -39.27 -46.73 1 1.00e+01 1.00e-02 3.02e+01 ... (remaining 15821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.281: 3956 0.281 - 0.562: 14 0.562 - 0.842: 6 0.842 - 1.123: 0 1.123 - 1.404: 4 Chirality restraints: 3980 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.00 -1.40 2.00e-02 2.50e+03 4.93e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.00 -1.40 2.00e-02 2.50e+03 4.93e+03 chirality pdb=" C1 NAG V 3 " pdb=" O4 NAG V 2 " pdb=" C2 NAG V 3 " pdb=" O5 NAG V 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-02 2.50e+03 1.00e+03 ... (remaining 3977 not shown) Planarity restraints: 4478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " -0.354 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG J 2 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " -0.107 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " 0.543 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " -0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " 0.354 2.00e-02 2.50e+03 3.05e-01 1.16e+03 pdb=" C7 NAG R 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " -0.543 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 2 " 0.294 2.00e-02 2.50e+03 2.53e-01 7.98e+02 pdb=" C7 NAG V 2 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG V 2 " -0.008 2.00e-02 2.50e+03 pdb=" N2 NAG V 2 " -0.430 2.00e-02 2.50e+03 pdb=" O7 NAG V 2 " 0.209 2.00e-02 2.50e+03 ... (remaining 4475 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 164 2.53 - 3.12: 18176 3.12 - 3.71: 37393 3.71 - 4.31: 55151 4.31 - 4.90: 90421 Nonbonded interactions: 201305 Sorted by model distance: nonbonded pdb=" O SER B 105 " pdb=" OG SER B 106 " model vdw 1.932 3.040 nonbonded pdb=" O SER D 105 " pdb=" OG SER D 106 " model vdw 1.932 3.040 nonbonded pdb=" NH1 ARG F 346 " pdb=" O PHE F 347 " model vdw 1.982 3.120 nonbonded pdb=" NH1 ARG E 346 " pdb=" O PHE E 347 " model vdw 1.982 3.120 nonbonded pdb=" O SER F 477 " pdb=" OG1 THR F 478 " model vdw 2.032 3.040 ... (remaining 201300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.780 Find NCS groups from input model: 0.430 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:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 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 : 0.012 0.628 26084 Z= 0.580 Angle : 1.500 71.289 35578 Z= 0.755 Chirality : 0.081 1.404 3980 Planarity : 0.014 0.305 4452 Dihedral : 15.887 88.421 10016 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 1.70 % Allowed : 9.48 % Favored : 88.82 % Rotamer: Outliers : 5.25 % Allowed : 9.39 % Favored : 85.37 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.89 (0.10), residues: 3060 helix: -4.47 (0.05), residues: 1608 sheet: -1.10 (0.39), residues: 160 loop : -3.34 (0.14), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 355 TYR 0.024 0.002 TYR B 385 PHE 0.016 0.002 PHE C 48 TRP 0.013 0.002 TRP B 302 HIS 0.006 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00818 (26022) covalent geometry : angle 1.04846 (35414) SS BOND : bond 0.31320 ( 16) SS BOND : angle 23.01539 ( 32) hydrogen bonds : bond 0.31498 ( 1062) hydrogen bonds : angle 9.36956 ( 3072) metal coordination : bond 0.09146 ( 2) link_BETA1-4 : bond 0.09804 ( 18) link_BETA1-4 : angle 17.28303 ( 54) link_NAG-ASN : bond 0.03954 ( 26) link_NAG-ASN : angle 10.17339 ( 78) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 573 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 GLN cc_start: 0.6201 (OUTLIER) cc_final: 0.5725 (tm130) REVERT: A 221 LYS cc_start: 0.4003 (OUTLIER) cc_final: 0.3636 (ttmm) REVERT: A 355 VAL cc_start: 0.8526 (t) cc_final: 0.7838 (p) REVERT: A 502 MET cc_start: 0.6348 (tpp) cc_final: 0.6014 (mmt) REVERT: B 102 GLN cc_start: 0.8042 (tp40) cc_final: 0.7454 (pm20) REVERT: B 190 MET cc_start: 0.7968 (tmm) cc_final: 0.7683 (tmm) REVERT: B 228 HIS cc_start: 0.7021 (t70) cc_final: 0.6692 (m-70) REVERT: B 313 LYS cc_start: 0.8972 (ttpt) cc_final: 0.8454 (tptt) REVERT: B 408 MET cc_start: 0.8774 (mmt) cc_final: 0.8544 (mmt) REVERT: B 556 ASN cc_start: 0.8524 (t0) cc_final: 0.7989 (t0) REVERT: B 637 ASP cc_start: 0.8174 (p0) cc_final: 0.7801 (m-30) REVERT: B 651 MET cc_start: 0.8884 (mmm) cc_final: 0.8523 (mmt) REVERT: B 736 GLN cc_start: 0.5057 (OUTLIER) cc_final: 0.3900 (tt0) REVERT: E 469 SER cc_start: 0.7193 (OUTLIER) cc_final: 0.6581 (t) REVERT: C 159 GLN cc_start: 0.6201 (OUTLIER) cc_final: 0.5725 (tm130) REVERT: C 221 LYS cc_start: 0.4004 (OUTLIER) cc_final: 0.3636 (ttmm) REVERT: C 355 VAL cc_start: 0.8524 (t) cc_final: 0.7834 (p) REVERT: C 502 MET cc_start: 0.6351 (tpp) cc_final: 0.6013 (mmt) REVERT: D 102 GLN cc_start: 0.8044 (tp40) cc_final: 0.7453 (pm20) REVERT: D 190 MET cc_start: 0.7967 (tmm) cc_final: 0.7684 (tmm) REVERT: D 228 HIS cc_start: 0.7022 (t70) cc_final: 0.6692 (m-70) REVERT: D 313 LYS cc_start: 0.8969 (ttpt) cc_final: 0.8452 (tptt) REVERT: D 408 MET cc_start: 0.8779 (mmt) cc_final: 0.8550 (mmt) REVERT: D 556 ASN cc_start: 0.8524 (t0) cc_final: 0.7991 (t0) REVERT: D 637 ASP cc_start: 0.8172 (p0) cc_final: 0.7802 (m-30) REVERT: D 651 MET cc_start: 0.8885 (mmm) cc_final: 0.8525 (mmt) REVERT: D 736 GLN cc_start: 0.5061 (OUTLIER) cc_final: 0.3905 (tt0) REVERT: F 469 SER cc_start: 0.7194 (OUTLIER) cc_final: 0.6586 (t) outliers start: 142 outliers final: 12 residues processed: 677 average time/residue: 0.5841 time to fit residues: 460.5841 Evaluate side-chains 272 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLN Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 438 SER Chi-restraints excluded: chain E residue 469 SER Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 438 SER Chi-restraints excluded: chain F residue 469 SER Chi-restraints excluded: chain F residue 489 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 9.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 194 GLN A 310 ASN A 340 ASN A 435 ASN A 531 GLN A 580 ASN B 51 ASN B 58 ASN B 61 ASN B 96 GLN B 101 GLN B 159 ASN B 175 GLN B 239 HIS B 277 ASN B 287 GLN B 378 HIS B 437 ASN B 472 GLN B 505 HIS B 586 ASN B 736 GLN E 394 ASN E 422 ASN E 440 ASN ** E 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS C 194 GLN C 310 ASN C 340 ASN C 435 ASN C 531 GLN C 580 ASN D 51 ASN D 58 ASN D 61 ASN D 96 GLN D 101 GLN D 159 ASN D 175 GLN D 239 HIS D 277 ASN D 287 GLN D 378 HIS D 437 ASN D 472 GLN D 505 HIS D 586 ASN D 736 GLN F 394 ASN F 422 ASN F 440 ASN ** F 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.162270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.109360 restraints weight = 44783.587| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.07 r_work: 0.3213 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 26084 Z= 0.204 Angle : 0.864 20.218 35578 Z= 0.419 Chirality : 0.052 0.467 3980 Planarity : 0.006 0.053 4452 Dihedral : 8.551 84.892 4294 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.36 % Favored : 94.38 % Rotamer: Outliers : 4.03 % Allowed : 17.37 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.56 (0.13), residues: 3060 helix: -2.21 (0.10), residues: 1696 sheet: -0.34 (0.45), residues: 130 loop : -2.65 (0.16), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 306 TYR 0.024 0.002 TYR A 316 PHE 0.025 0.002 PHE D 746 TRP 0.016 0.001 TRP F 436 HIS 0.007 0.001 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.00458 (26022) covalent geometry : angle 0.80992 (35414) SS BOND : bond 0.00370 ( 16) SS BOND : angle 1.94974 ( 32) hydrogen bonds : bond 0.06352 ( 1062) hydrogen bonds : angle 4.96318 ( 3072) metal coordination : bond 0.00276 ( 2) link_BETA1-4 : bond 0.00717 ( 18) link_BETA1-4 : angle 2.72578 ( 54) link_NAG-ASN : bond 0.01437 ( 26) link_NAG-ASN : angle 5.97276 ( 78) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 312 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ILE cc_start: 0.8339 (tp) cc_final: 0.8135 (tp) REVERT: A 365 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7928 (mm-40) REVERT: A 479 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8352 (tm-30) REVERT: A 583 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: B 102 GLN cc_start: 0.8502 (tp40) cc_final: 0.7766 (pm20) REVERT: B 190 MET cc_start: 0.8660 (tmm) cc_final: 0.8445 (tmm) REVERT: B 293 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8316 (p) REVERT: B 297 MET cc_start: 0.8121 (mtp) cc_final: 0.7894 (mtm) REVERT: B 313 LYS cc_start: 0.9051 (ttpt) cc_final: 0.8560 (tptt) REVERT: B 343 VAL cc_start: 0.6487 (OUTLIER) cc_final: 0.6272 (p) REVERT: B 556 ASN cc_start: 0.8582 (t0) cc_final: 0.8062 (t0) REVERT: B 651 MET cc_start: 0.9498 (mmm) cc_final: 0.9106 (mmt) REVERT: B 736 GLN cc_start: 0.5292 (OUTLIER) cc_final: 0.4114 (tt0) REVERT: E 399 SER cc_start: 0.5310 (OUTLIER) cc_final: 0.5102 (m) REVERT: E 439 ASN cc_start: 0.7945 (t0) cc_final: 0.7413 (p0) REVERT: E 464 PHE cc_start: 0.5361 (m-80) cc_final: 0.5096 (m-80) REVERT: E 488 CYS cc_start: 0.6062 (t) cc_final: 0.5463 (p) REVERT: C 92 ILE cc_start: 0.8335 (tp) cc_final: 0.8131 (tp) REVERT: C 479 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8354 (tm-30) REVERT: C 583 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: D 102 GLN cc_start: 0.8505 (tp40) cc_final: 0.7767 (pm20) REVERT: D 190 MET cc_start: 0.8654 (tmm) cc_final: 0.8438 (tmm) REVERT: D 293 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8311 (p) REVERT: D 297 MET cc_start: 0.8127 (mtp) cc_final: 0.7899 (mtm) REVERT: D 313 LYS cc_start: 0.9051 (ttpt) cc_final: 0.8561 (tptt) REVERT: D 343 VAL cc_start: 0.6483 (OUTLIER) cc_final: 0.6268 (p) REVERT: D 556 ASN cc_start: 0.8584 (t0) cc_final: 0.8063 (t0) REVERT: D 651 MET cc_start: 0.9492 (mmm) cc_final: 0.9101 (mmt) REVERT: D 736 GLN cc_start: 0.5296 (OUTLIER) cc_final: 0.4120 (tt0) REVERT: F 399 SER cc_start: 0.5309 (OUTLIER) cc_final: 0.5101 (m) REVERT: F 439 ASN cc_start: 0.7946 (t0) cc_final: 0.7416 (p0) REVERT: F 464 PHE cc_start: 0.5367 (m-80) cc_final: 0.5100 (m-80) REVERT: F 488 CYS cc_start: 0.6077 (t) cc_final: 0.5467 (p) outliers start: 109 outliers final: 42 residues processed: 387 average time/residue: 0.4949 time to fit residues: 229.4090 Evaluate side-chains 293 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 240 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 365 GLN Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 572 LYS Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 399 SER Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 572 LYS Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 686 THR Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 763 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 399 SER Chi-restraints excluded: chain F residue 430 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 251 optimal weight: 10.0000 chunk 222 optimal weight: 0.9980 chunk 229 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 192 optimal weight: 0.1980 chunk 255 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN B 228 HIS B 599 ASN E 487 ASN E 501 ASN C 435 ASN D 228 HIS D 599 ASN F 487 ASN F 501 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.161090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.107618 restraints weight = 44403.098| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 3.03 r_work: 0.3196 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 26084 Z= 0.161 Angle : 0.737 17.337 35578 Z= 0.354 Chirality : 0.048 0.440 3980 Planarity : 0.005 0.058 4452 Dihedral : 7.546 59.981 4264 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.69 % Favored : 94.05 % Rotamer: Outliers : 4.21 % Allowed : 19.59 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.14), residues: 3060 helix: -1.07 (0.12), residues: 1704 sheet: -0.46 (0.46), residues: 118 loop : -2.28 (0.16), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 306 TYR 0.019 0.002 TYR A 224 PHE 0.016 0.001 PHE D 746 TRP 0.018 0.001 TRP E 436 HIS 0.031 0.002 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00364 (26022) covalent geometry : angle 0.68521 (35414) SS BOND : bond 0.00245 ( 16) SS BOND : angle 1.23129 ( 32) hydrogen bonds : bond 0.05229 ( 1062) hydrogen bonds : angle 4.57762 ( 3072) metal coordination : bond 0.00189 ( 2) link_BETA1-4 : bond 0.00656 ( 18) link_BETA1-4 : angle 2.15461 ( 54) link_NAG-ASN : bond 0.01568 ( 26) link_NAG-ASN : angle 5.54712 ( 78) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 296 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8231 (mtm) cc_final: 0.7971 (mtp) REVERT: A 479 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8385 (tm-30) REVERT: A 583 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.7340 (m-80) REVERT: B 26 LYS cc_start: 0.7940 (tttt) cc_final: 0.7466 (tmtt) REVERT: B 42 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8235 (mp10) REVERT: B 102 GLN cc_start: 0.8587 (tp40) cc_final: 0.7937 (pm20) REVERT: B 293 VAL cc_start: 0.8765 (OUTLIER) cc_final: 0.8492 (p) REVERT: B 297 MET cc_start: 0.8107 (mtp) cc_final: 0.7750 (mtm) REVERT: B 313 LYS cc_start: 0.9113 (ttpt) cc_final: 0.8631 (tptt) REVERT: B 332 MET cc_start: 0.8512 (ptm) cc_final: 0.8214 (ppp) REVERT: B 556 ASN cc_start: 0.8597 (t0) cc_final: 0.8040 (t0) REVERT: B 651 MET cc_start: 0.9462 (mmm) cc_final: 0.9115 (mmt) REVERT: B 736 GLN cc_start: 0.4745 (OUTLIER) cc_final: 0.3972 (tp40) REVERT: E 464 PHE cc_start: 0.5464 (m-80) cc_final: 0.4991 (t80) REVERT: E 488 CYS cc_start: 0.6048 (t) cc_final: 0.5639 (p) REVERT: C 124 MET cc_start: 0.8226 (mtm) cc_final: 0.7963 (mtp) REVERT: C 479 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8384 (tm-30) REVERT: C 583 TYR cc_start: 0.7794 (OUTLIER) cc_final: 0.7339 (m-80) REVERT: D 26 LYS cc_start: 0.7939 (tttt) cc_final: 0.7464 (tmtt) REVERT: D 42 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8233 (mp10) REVERT: D 102 GLN cc_start: 0.8586 (tp40) cc_final: 0.7939 (pm20) REVERT: D 293 VAL cc_start: 0.8761 (OUTLIER) cc_final: 0.8488 (p) REVERT: D 297 MET cc_start: 0.8111 (mtp) cc_final: 0.7752 (mtm) REVERT: D 313 LYS cc_start: 0.9109 (ttpt) cc_final: 0.8634 (tptt) REVERT: D 332 MET cc_start: 0.8514 (ptm) cc_final: 0.8217 (ppp) REVERT: D 556 ASN cc_start: 0.8594 (t0) cc_final: 0.8035 (t0) REVERT: D 651 MET cc_start: 0.9463 (mmm) cc_final: 0.9120 (mmt) REVERT: D 736 GLN cc_start: 0.4743 (OUTLIER) cc_final: 0.3970 (tp40) REVERT: F 464 PHE cc_start: 0.5477 (m-80) cc_final: 0.4998 (t80) REVERT: F 488 CYS cc_start: 0.6047 (t) cc_final: 0.5640 (p) outliers start: 114 outliers final: 48 residues processed: 377 average time/residue: 0.5524 time to fit residues: 247.7595 Evaluate side-chains 299 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 243 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 90 PHE Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 147 optimal weight: 20.0000 chunk 42 optimal weight: 0.6980 chunk 87 optimal weight: 0.1980 chunk 252 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 26 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 130 ASN A 531 GLN B 61 ASN B 228 HIS B 493 HIS B 599 ASN E 474 GLN E 501 ASN C 108 HIS C 130 ASN C 531 GLN D 61 ASN D 228 HIS D 493 HIS D 599 ASN F 450 ASN F 474 GLN F 501 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.162445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.107637 restraints weight = 44066.578| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.07 r_work: 0.3200 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26084 Z= 0.136 Angle : 0.702 19.007 35578 Z= 0.334 Chirality : 0.047 0.420 3980 Planarity : 0.004 0.035 4452 Dihedral : 6.884 59.472 4264 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.46 % Favored : 94.28 % Rotamer: Outliers : 3.99 % Allowed : 20.92 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.15), residues: 3060 helix: -0.53 (0.12), residues: 1708 sheet: -0.17 (0.43), residues: 138 loop : -1.95 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 306 TYR 0.025 0.001 TYR A 578 PHE 0.013 0.001 PHE D 746 TRP 0.020 0.001 TRP F 436 HIS 0.007 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00302 (26022) covalent geometry : angle 0.64774 (35414) SS BOND : bond 0.00794 ( 16) SS BOND : angle 2.04008 ( 32) hydrogen bonds : bond 0.04498 ( 1062) hydrogen bonds : angle 4.42710 ( 3072) metal coordination : bond 0.00039 ( 2) link_BETA1-4 : bond 0.00539 ( 18) link_BETA1-4 : angle 1.94714 ( 54) link_NAG-ASN : bond 0.01287 ( 26) link_NAG-ASN : angle 5.47372 ( 78) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 272 time to evaluate : 0.802 Fit side-chains REVERT: A 479 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8381 (tm-30) REVERT: A 583 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.7265 (m-80) REVERT: B 26 LYS cc_start: 0.7904 (tttt) cc_final: 0.7423 (mtpp) REVERT: B 42 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8065 (mp10) REVERT: B 102 GLN cc_start: 0.8516 (tp40) cc_final: 0.7966 (pm20) REVERT: B 293 VAL cc_start: 0.8572 (OUTLIER) cc_final: 0.8253 (p) REVERT: B 297 MET cc_start: 0.8142 (mtp) cc_final: 0.7757 (mtm) REVERT: B 313 LYS cc_start: 0.9116 (ttpt) cc_final: 0.8615 (tptt) REVERT: B 332 MET cc_start: 0.8445 (ptm) cc_final: 0.8117 (ppp) REVERT: B 556 ASN cc_start: 0.8612 (t0) cc_final: 0.8092 (t0) REVERT: B 651 MET cc_start: 0.9427 (mmm) cc_final: 0.9131 (mmt) REVERT: B 713 ASP cc_start: 0.8741 (m-30) cc_final: 0.8504 (m-30) REVERT: B 736 GLN cc_start: 0.4911 (OUTLIER) cc_final: 0.4312 (tp40) REVERT: E 464 PHE cc_start: 0.5815 (m-80) cc_final: 0.5165 (t80) REVERT: C 479 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8381 (tm-30) REVERT: C 583 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.7262 (m-80) REVERT: D 26 LYS cc_start: 0.7899 (tttt) cc_final: 0.7417 (mtpp) REVERT: D 42 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8069 (mp10) REVERT: D 102 GLN cc_start: 0.8521 (tp40) cc_final: 0.7970 (pm20) REVERT: D 293 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8337 (p) REVERT: D 297 MET cc_start: 0.8146 (mtp) cc_final: 0.7941 (mtm) REVERT: D 313 LYS cc_start: 0.9115 (ttpt) cc_final: 0.8613 (tptt) REVERT: D 332 MET cc_start: 0.8448 (ptm) cc_final: 0.8120 (ppp) REVERT: D 556 ASN cc_start: 0.8608 (t0) cc_final: 0.8092 (t0) REVERT: D 651 MET cc_start: 0.9419 (mmm) cc_final: 0.9125 (mmt) REVERT: D 713 ASP cc_start: 0.8742 (m-30) cc_final: 0.8504 (m-30) REVERT: D 736 GLN cc_start: 0.4909 (OUTLIER) cc_final: 0.4311 (tp40) REVERT: F 464 PHE cc_start: 0.5823 (m-80) cc_final: 0.5167 (t80) outliers start: 108 outliers final: 50 residues processed: 348 average time/residue: 0.5079 time to fit residues: 210.5118 Evaluate side-chains 297 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 239 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 686 THR Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 196 optimal weight: 0.0980 chunk 42 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 245 optimal weight: 10.0000 chunk 253 optimal weight: 0.5980 chunk 219 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 232 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 130 ASN A 297 ASN B 61 ASN B 599 ASN E 501 ASN C 108 HIS C 130 ASN C 297 ASN D 61 ASN F 501 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.161956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.104098 restraints weight = 44602.267| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.43 r_work: 0.3280 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26084 Z= 0.121 Angle : 0.686 19.225 35578 Z= 0.324 Chirality : 0.046 0.404 3980 Planarity : 0.004 0.032 4452 Dihedral : 6.448 59.260 4260 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.52 % Favored : 94.22 % Rotamer: Outliers : 3.70 % Allowed : 21.14 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.15), residues: 3060 helix: -0.21 (0.13), residues: 1718 sheet: -0.14 (0.47), residues: 114 loop : -1.76 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 306 TYR 0.021 0.001 TYR A 578 PHE 0.011 0.001 PHE D 684 TRP 0.019 0.001 TRP E 436 HIS 0.013 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00263 (26022) covalent geometry : angle 0.63148 (35414) SS BOND : bond 0.00788 ( 16) SS BOND : angle 2.06676 ( 32) hydrogen bonds : bond 0.04107 ( 1062) hydrogen bonds : angle 4.34085 ( 3072) metal coordination : bond 0.00002 ( 2) link_BETA1-4 : bond 0.00506 ( 18) link_BETA1-4 : angle 1.87942 ( 54) link_NAG-ASN : bond 0.01222 ( 26) link_NAG-ASN : angle 5.40783 ( 78) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 268 time to evaluate : 0.944 Fit side-chains REVERT: A 137 MET cc_start: 0.8474 (mtm) cc_final: 0.8194 (ptm) REVERT: A 583 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: B 26 LYS cc_start: 0.7977 (tttt) cc_final: 0.7518 (mtpp) REVERT: B 42 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8128 (mp10) REVERT: B 102 GLN cc_start: 0.8561 (tp40) cc_final: 0.8043 (pm20) REVERT: B 297 MET cc_start: 0.8188 (mtp) cc_final: 0.7784 (mtm) REVERT: B 313 LYS cc_start: 0.9129 (ttpt) cc_final: 0.8613 (tptt) REVERT: B 332 MET cc_start: 0.8415 (ptm) cc_final: 0.8212 (ppp) REVERT: B 556 ASN cc_start: 0.8600 (t0) cc_final: 0.8121 (t0) REVERT: B 651 MET cc_start: 0.9422 (mmm) cc_final: 0.9129 (mmt) REVERT: B 713 ASP cc_start: 0.8846 (m-30) cc_final: 0.8624 (m-30) REVERT: B 736 GLN cc_start: 0.4796 (OUTLIER) cc_final: 0.4210 (tp40) REVERT: E 464 PHE cc_start: 0.5951 (m-80) cc_final: 0.5246 (t80) REVERT: C 137 MET cc_start: 0.8477 (mtm) cc_final: 0.8197 (ptm) REVERT: C 583 TYR cc_start: 0.7677 (OUTLIER) cc_final: 0.7241 (m-80) REVERT: D 26 LYS cc_start: 0.7975 (tttt) cc_final: 0.7516 (mtpp) REVERT: D 42 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: D 102 GLN cc_start: 0.8558 (tp40) cc_final: 0.8041 (pm20) REVERT: D 297 MET cc_start: 0.8188 (mtp) cc_final: 0.7781 (mtm) REVERT: D 313 LYS cc_start: 0.9128 (ttpt) cc_final: 0.8612 (tptt) REVERT: D 332 MET cc_start: 0.8415 (ptm) cc_final: 0.8214 (ppp) REVERT: D 556 ASN cc_start: 0.8601 (t0) cc_final: 0.8123 (t0) REVERT: D 651 MET cc_start: 0.9419 (mmm) cc_final: 0.9127 (mmt) REVERT: D 713 ASP cc_start: 0.8848 (m-30) cc_final: 0.8615 (m-30) REVERT: D 736 GLN cc_start: 0.4794 (OUTLIER) cc_final: 0.4207 (tp40) REVERT: F 464 PHE cc_start: 0.5956 (m-80) cc_final: 0.5245 (t80) REVERT: F 466 ARG cc_start: 0.5018 (tpt-90) cc_final: 0.4818 (tpt-90) outliers start: 100 outliers final: 48 residues processed: 344 average time/residue: 0.5215 time to fit residues: 213.1514 Evaluate side-chains 291 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 237 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 736 GLN Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 478 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 143 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 9 optimal weight: 20.0000 chunk 150 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 192 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 297 ASN A 435 ASN B 61 ASN B 599 ASN E 450 ASN E 501 ASN C 108 HIS C 297 ASN C 435 ASN D 61 ASN F 501 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.160940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.101921 restraints weight = 44343.657| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.36 r_work: 0.3260 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26084 Z= 0.144 Angle : 0.702 18.703 35578 Z= 0.335 Chirality : 0.046 0.395 3980 Planarity : 0.004 0.034 4452 Dihedral : 6.014 58.093 4260 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.42 % Favored : 94.31 % Rotamer: Outliers : 3.62 % Allowed : 21.58 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.15), residues: 3060 helix: 0.05 (0.13), residues: 1696 sheet: 0.10 (0.45), residues: 130 loop : -1.60 (0.17), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 306 TYR 0.020 0.001 TYR A 488 PHE 0.013 0.001 PHE D 684 TRP 0.023 0.001 TRP F 436 HIS 0.006 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00330 (26022) covalent geometry : angle 0.65251 (35414) SS BOND : bond 0.00630 ( 16) SS BOND : angle 1.60110 ( 32) hydrogen bonds : bond 0.04406 ( 1062) hydrogen bonds : angle 4.35725 ( 3072) metal coordination : bond 0.00069 ( 2) link_BETA1-4 : bond 0.00466 ( 18) link_BETA1-4 : angle 1.87393 ( 54) link_NAG-ASN : bond 0.01210 ( 26) link_NAG-ASN : angle 5.30437 ( 78) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 249 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8486 (mtm) cc_final: 0.8200 (ptm) REVERT: A 583 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.7013 (m-10) REVERT: B 26 LYS cc_start: 0.7958 (tttt) cc_final: 0.7525 (mtpp) REVERT: B 42 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8108 (mp10) REVERT: B 60 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8264 (mm-40) REVERT: B 62 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.7085 (ptm) REVERT: B 102 GLN cc_start: 0.8577 (tp40) cc_final: 0.8043 (pm20) REVERT: B 313 LYS cc_start: 0.9138 (ttpt) cc_final: 0.8629 (tptt) REVERT: B 332 MET cc_start: 0.8503 (ptm) cc_final: 0.8172 (ppp) REVERT: B 556 ASN cc_start: 0.8658 (t0) cc_final: 0.8157 (t0) REVERT: B 651 MET cc_start: 0.9437 (mmm) cc_final: 0.9166 (mmt) REVERT: B 706 MET cc_start: 0.8751 (ttp) cc_final: 0.8532 (ttt) REVERT: B 713 ASP cc_start: 0.8902 (m-30) cc_final: 0.8634 (m-30) REVERT: E 436 TRP cc_start: 0.6448 (p90) cc_final: 0.6239 (p90) REVERT: E 464 PHE cc_start: 0.5930 (m-80) cc_final: 0.5195 (t80) REVERT: E 489 TYR cc_start: 0.6977 (OUTLIER) cc_final: 0.6339 (m-80) REVERT: C 137 MET cc_start: 0.8495 (mtm) cc_final: 0.8209 (ptm) REVERT: C 583 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.7045 (m-10) REVERT: D 26 LYS cc_start: 0.7941 (tttt) cc_final: 0.7504 (mtpp) REVERT: D 42 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8116 (mp10) REVERT: D 60 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8270 (mm-40) REVERT: D 62 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7090 (ptm) REVERT: D 102 GLN cc_start: 0.8583 (tp40) cc_final: 0.8051 (pm20) REVERT: D 313 LYS cc_start: 0.9141 (ttpt) cc_final: 0.8632 (tptt) REVERT: D 332 MET cc_start: 0.8506 (ptm) cc_final: 0.8173 (ppp) REVERT: D 556 ASN cc_start: 0.8662 (t0) cc_final: 0.8162 (t0) REVERT: D 651 MET cc_start: 0.9435 (mmm) cc_final: 0.9163 (mmt) REVERT: D 706 MET cc_start: 0.8753 (ttp) cc_final: 0.8534 (ttt) REVERT: D 713 ASP cc_start: 0.8904 (m-30) cc_final: 0.8636 (m-30) REVERT: F 409 GLN cc_start: 0.7100 (mt0) cc_final: 0.6408 (tt0) REVERT: F 464 PHE cc_start: 0.5982 (m-80) cc_final: 0.5199 (t80) REVERT: F 489 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.6331 (m-80) outliers start: 98 outliers final: 62 residues processed: 326 average time/residue: 0.5149 time to fit residues: 200.2520 Evaluate side-chains 299 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 229 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 686 THR Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 744 ILE Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 489 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 230 optimal weight: 0.0970 chunk 250 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 202 optimal weight: 8.9990 chunk 187 optimal weight: 0.1980 chunk 255 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 243 optimal weight: 0.7980 chunk 144 optimal weight: 20.0000 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 435 ASN B 61 ASN E 501 ASN C 108 HIS C 297 ASN C 435 ASN D 61 ASN F 501 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.159651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.105999 restraints weight = 44174.361| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.89 r_work: 0.3186 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 26084 Z= 0.145 Angle : 0.703 18.689 35578 Z= 0.335 Chirality : 0.047 0.444 3980 Planarity : 0.004 0.046 4452 Dihedral : 5.818 57.799 4254 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.52 % Favored : 94.22 % Rotamer: Outliers : 3.62 % Allowed : 21.77 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.15), residues: 3060 helix: 0.15 (0.13), residues: 1708 sheet: -0.24 (0.46), residues: 118 loop : -1.54 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 306 TYR 0.017 0.001 TYR C 488 PHE 0.013 0.001 PHE B 684 TRP 0.022 0.001 TRP F 436 HIS 0.013 0.001 HIS C 108 Details of bonding type rmsd covalent geometry : bond 0.00336 (26022) covalent geometry : angle 0.65377 (35414) SS BOND : bond 0.01109 ( 16) SS BOND : angle 1.91348 ( 32) hydrogen bonds : bond 0.04276 ( 1062) hydrogen bonds : angle 4.35393 ( 3072) metal coordination : bond 0.00052 ( 2) link_BETA1-4 : bond 0.00494 ( 18) link_BETA1-4 : angle 1.84695 ( 54) link_NAG-ASN : bond 0.01090 ( 26) link_NAG-ASN : angle 5.24450 ( 78) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 239 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 LEU cc_start: 0.7102 (mt) cc_final: 0.6751 (pp) REVERT: A 137 MET cc_start: 0.8422 (mtm) cc_final: 0.8111 (ptm) REVERT: A 583 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6868 (m-10) REVERT: B 26 LYS cc_start: 0.7807 (tttt) cc_final: 0.7435 (mtpp) REVERT: B 42 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8060 (mp10) REVERT: B 62 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7098 (ptm) REVERT: B 102 GLN cc_start: 0.8532 (tp40) cc_final: 0.8034 (pm20) REVERT: B 313 LYS cc_start: 0.9145 (ttpt) cc_final: 0.8645 (tptt) REVERT: B 332 MET cc_start: 0.8484 (ptm) cc_final: 0.8250 (ppp) REVERT: B 345 HIS cc_start: 0.6885 (t-170) cc_final: 0.6342 (m-70) REVERT: B 556 ASN cc_start: 0.8701 (t0) cc_final: 0.8174 (t0) REVERT: B 651 MET cc_start: 0.9381 (mmm) cc_final: 0.9125 (mmt) REVERT: B 706 MET cc_start: 0.8687 (ttp) cc_final: 0.8468 (ttt) REVERT: B 713 ASP cc_start: 0.8769 (m-30) cc_final: 0.8501 (m-30) REVERT: E 464 PHE cc_start: 0.6174 (m-80) cc_final: 0.5264 (t80) REVERT: E 489 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.6230 (m-80) REVERT: C 21 LEU cc_start: 0.7106 (mt) cc_final: 0.6753 (pp) REVERT: C 137 MET cc_start: 0.8427 (mtm) cc_final: 0.8115 (ptm) REVERT: C 583 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.6840 (m-10) REVERT: D 26 LYS cc_start: 0.7831 (tttt) cc_final: 0.7459 (mtpp) REVERT: D 42 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8066 (mp10) REVERT: D 62 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7088 (ptm) REVERT: D 102 GLN cc_start: 0.8540 (tp40) cc_final: 0.8037 (pm20) REVERT: D 313 LYS cc_start: 0.9147 (ttpt) cc_final: 0.8647 (tptt) REVERT: D 332 MET cc_start: 0.8489 (ptm) cc_final: 0.8258 (ppp) REVERT: D 345 HIS cc_start: 0.6881 (t-170) cc_final: 0.6336 (m-70) REVERT: D 556 ASN cc_start: 0.8697 (t0) cc_final: 0.8160 (t0) REVERT: D 651 MET cc_start: 0.9378 (mmm) cc_final: 0.9124 (mmt) REVERT: D 706 MET cc_start: 0.8688 (ttp) cc_final: 0.8469 (ttt) REVERT: D 713 ASP cc_start: 0.8765 (m-30) cc_final: 0.8496 (m-30) REVERT: F 409 GLN cc_start: 0.7151 (mt0) cc_final: 0.6490 (tt0) REVERT: F 464 PHE cc_start: 0.6150 (m-80) cc_final: 0.5365 (t80) REVERT: F 466 ARG cc_start: 0.5139 (tpt-90) cc_final: 0.4714 (tpt-90) REVERT: F 489 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6217 (m-80) outliers start: 98 outliers final: 63 residues processed: 312 average time/residue: 0.5076 time to fit residues: 188.9485 Evaluate side-chains 307 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 236 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain B residue 42 GLN Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 488 CYS Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 501 ASN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 686 THR Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 744 ILE Chi-restraints excluded: chain D residue 763 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 488 CYS Chi-restraints excluded: chain F residue 489 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 203 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 216 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 210 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 233 optimal weight: 0.6980 chunk 250 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 108 HIS A 297 ASN A 435 ASN E 501 ASN C 297 ASN C 435 ASN F 501 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.158580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.105002 restraints weight = 44576.488| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.04 r_work: 0.3149 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26084 Z= 0.179 Angle : 0.728 18.621 35578 Z= 0.349 Chirality : 0.048 0.397 3980 Planarity : 0.004 0.044 4452 Dihedral : 5.819 57.394 4254 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.36 % Favored : 94.38 % Rotamer: Outliers : 3.14 % Allowed : 22.21 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.15), residues: 3060 helix: 0.16 (0.13), residues: 1712 sheet: 0.12 (0.44), residues: 126 loop : -1.49 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 306 TYR 0.020 0.002 TYR A 578 PHE 0.022 0.001 PHE D 72 TRP 0.025 0.001 TRP E 436 HIS 0.033 0.002 HIS C 108 Details of bonding type rmsd covalent geometry : bond 0.00423 (26022) covalent geometry : angle 0.68104 (35414) SS BOND : bond 0.00840 ( 16) SS BOND : angle 1.69216 ( 32) hydrogen bonds : bond 0.04604 ( 1062) hydrogen bonds : angle 4.42224 ( 3072) metal coordination : bond 0.00056 ( 2) link_BETA1-4 : bond 0.00456 ( 18) link_BETA1-4 : angle 1.85978 ( 54) link_NAG-ASN : bond 0.01161 ( 26) link_NAG-ASN : angle 5.23903 ( 78) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 248 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 550 PHE cc_start: 0.6940 (m-80) cc_final: 0.6563 (m-80) REVERT: A 583 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.6974 (m-10) REVERT: B 26 LYS cc_start: 0.7845 (tttt) cc_final: 0.7456 (mtpp) REVERT: B 42 GLN cc_start: 0.8410 (mt0) cc_final: 0.8041 (mp10) REVERT: B 62 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.7060 (ptm) REVERT: B 83 TYR cc_start: 0.7771 (m-80) cc_final: 0.7393 (m-80) REVERT: B 102 GLN cc_start: 0.8584 (tp40) cc_final: 0.8012 (pm20) REVERT: B 332 MET cc_start: 0.8513 (ptm) cc_final: 0.8265 (ppp) REVERT: B 345 HIS cc_start: 0.7023 (t-170) cc_final: 0.6353 (m170) REVERT: B 556 ASN cc_start: 0.8741 (t0) cc_final: 0.8198 (t0) REVERT: B 651 MET cc_start: 0.9393 (mmm) cc_final: 0.9118 (mmt) REVERT: B 706 MET cc_start: 0.8749 (ttp) cc_final: 0.8535 (ttt) REVERT: B 713 ASP cc_start: 0.8815 (m-30) cc_final: 0.8549 (m-30) REVERT: E 464 PHE cc_start: 0.6201 (m-80) cc_final: 0.5245 (t80) REVERT: E 489 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.6290 (m-80) REVERT: C 550 PHE cc_start: 0.6928 (m-80) cc_final: 0.6464 (m-80) REVERT: C 583 TYR cc_start: 0.7428 (OUTLIER) cc_final: 0.6970 (m-10) REVERT: D 26 LYS cc_start: 0.7843 (tttt) cc_final: 0.7452 (mtpp) REVERT: D 42 GLN cc_start: 0.8411 (mt0) cc_final: 0.8039 (mp10) REVERT: D 62 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.7064 (ptm) REVERT: D 83 TYR cc_start: 0.7767 (m-80) cc_final: 0.7386 (m-80) REVERT: D 102 GLN cc_start: 0.8588 (tp40) cc_final: 0.8015 (pm20) REVERT: D 332 MET cc_start: 0.8516 (ptm) cc_final: 0.8266 (ppp) REVERT: D 345 HIS cc_start: 0.7016 (t-170) cc_final: 0.6344 (m170) REVERT: D 556 ASN cc_start: 0.8718 (t0) cc_final: 0.8164 (t0) REVERT: D 651 MET cc_start: 0.9392 (mmm) cc_final: 0.9123 (mmt) REVERT: D 706 MET cc_start: 0.8747 (ttp) cc_final: 0.8532 (ttt) REVERT: D 713 ASP cc_start: 0.8807 (m-30) cc_final: 0.8541 (m-30) REVERT: F 409 GLN cc_start: 0.7151 (mt0) cc_final: 0.6497 (tt0) REVERT: F 464 PHE cc_start: 0.6181 (m-80) cc_final: 0.5384 (t80) REVERT: F 489 TYR cc_start: 0.7017 (OUTLIER) cc_final: 0.6280 (m-80) outliers start: 85 outliers final: 66 residues processed: 316 average time/residue: 0.4967 time to fit residues: 187.8055 Evaluate side-chains 289 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 217 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 488 CYS Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 686 THR Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 763 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 488 CYS Chi-restraints excluded: chain F residue 489 TYR Chi-restraints excluded: chain F residue 501 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 296 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 276 optimal weight: 0.0670 chunk 238 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 270 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 232 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 137 optimal weight: 30.0000 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 297 ASN A 435 ASN E 501 ASN C 8 ASN C 108 HIS C 297 ASN C 435 ASN F 501 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.160272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101579 restraints weight = 44114.782| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.31 r_work: 0.3238 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26084 Z= 0.131 Angle : 0.696 18.661 35578 Z= 0.333 Chirality : 0.047 0.399 3980 Planarity : 0.004 0.045 4452 Dihedral : 5.704 57.678 4254 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.13 % Favored : 94.61 % Rotamer: Outliers : 3.14 % Allowed : 22.88 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 3060 helix: 0.30 (0.13), residues: 1712 sheet: 0.19 (0.50), residues: 94 loop : -1.42 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 306 TYR 0.019 0.001 TYR A 488 PHE 0.032 0.001 PHE D 72 TRP 0.026 0.001 TRP E 436 HIS 0.011 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00296 (26022) covalent geometry : angle 0.64868 (35414) SS BOND : bond 0.00648 ( 16) SS BOND : angle 1.44583 ( 32) hydrogen bonds : bond 0.04201 ( 1062) hydrogen bonds : angle 4.36833 ( 3072) metal coordination : bond 0.00004 ( 2) link_BETA1-4 : bond 0.00442 ( 18) link_BETA1-4 : angle 1.77906 ( 54) link_NAG-ASN : bond 0.01134 ( 26) link_NAG-ASN : angle 5.17976 ( 78) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 225 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 MET cc_start: 0.8450 (mtm) cc_final: 0.8162 (ptm) REVERT: A 583 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.6977 (m-10) REVERT: B 26 LYS cc_start: 0.7960 (tttt) cc_final: 0.7584 (mtpp) REVERT: B 62 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.7056 (ptm) REVERT: B 79 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8321 (tp) REVERT: B 83 TYR cc_start: 0.7698 (m-80) cc_final: 0.7490 (m-80) REVERT: B 102 GLN cc_start: 0.8602 (tp40) cc_final: 0.8054 (pm20) REVERT: B 332 MET cc_start: 0.8486 (ptm) cc_final: 0.8235 (ppp) REVERT: B 345 HIS cc_start: 0.6947 (t-170) cc_final: 0.6372 (m170) REVERT: B 556 ASN cc_start: 0.8786 (t0) cc_final: 0.8259 (t0) REVERT: B 651 MET cc_start: 0.9396 (mmm) cc_final: 0.9150 (mmt) REVERT: B 706 MET cc_start: 0.8756 (ttp) cc_final: 0.8468 (ttm) REVERT: B 713 ASP cc_start: 0.8887 (m-30) cc_final: 0.8610 (m-30) REVERT: E 464 PHE cc_start: 0.6216 (m-80) cc_final: 0.5224 (t80) REVERT: E 489 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.6363 (m-80) REVERT: C 137 MET cc_start: 0.8464 (mtm) cc_final: 0.8205 (ptm) REVERT: C 583 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6904 (m-10) REVERT: D 26 LYS cc_start: 0.7903 (tttt) cc_final: 0.7522 (mtpp) REVERT: D 62 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.7067 (ptm) REVERT: D 79 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8267 (tp) REVERT: D 83 TYR cc_start: 0.7698 (m-80) cc_final: 0.7489 (m-80) REVERT: D 102 GLN cc_start: 0.8608 (tp40) cc_final: 0.8054 (pm20) REVERT: D 332 MET cc_start: 0.8490 (ptm) cc_final: 0.8239 (ppp) REVERT: D 345 HIS cc_start: 0.6938 (t-170) cc_final: 0.6354 (m170) REVERT: D 556 ASN cc_start: 0.8773 (t0) cc_final: 0.8242 (t0) REVERT: D 651 MET cc_start: 0.9394 (mmm) cc_final: 0.9150 (mmt) REVERT: D 706 MET cc_start: 0.8759 (ttp) cc_final: 0.8469 (ttm) REVERT: D 713 ASP cc_start: 0.8883 (m-30) cc_final: 0.8604 (m-30) REVERT: F 464 PHE cc_start: 0.6193 (m-80) cc_final: 0.5370 (t80) REVERT: F 489 TYR cc_start: 0.7122 (OUTLIER) cc_final: 0.6352 (m-80) outliers start: 85 outliers final: 55 residues processed: 294 average time/residue: 0.4861 time to fit residues: 172.2563 Evaluate side-chains 288 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 225 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 488 CYS Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 108 HIS Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 763 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 488 CYS Chi-restraints excluded: chain F residue 489 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 88 optimal weight: 0.9980 chunk 292 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 289 optimal weight: 30.0000 chunk 250 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 68 optimal weight: 0.0060 chunk 170 optimal weight: 6.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 435 ASN E 501 ASN ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 435 ASN F 501 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.156783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.098853 restraints weight = 44079.136| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.36 r_work: 0.3199 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 26084 Z= 0.215 Angle : 0.750 18.286 35578 Z= 0.363 Chirality : 0.050 0.394 3980 Planarity : 0.004 0.050 4452 Dihedral : 5.885 57.109 4254 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.65 % Favored : 94.08 % Rotamer: Outliers : 2.81 % Allowed : 23.28 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.15), residues: 3060 helix: 0.17 (0.13), residues: 1714 sheet: 0.06 (0.45), residues: 126 loop : -1.51 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 306 TYR 0.022 0.002 TYR B 83 PHE 0.029 0.002 PHE D 72 TRP 0.029 0.002 TRP F 436 HIS 0.015 0.002 HIS C 108 Details of bonding type rmsd covalent geometry : bond 0.00513 (26022) covalent geometry : angle 0.70599 (35414) SS BOND : bond 0.00711 ( 16) SS BOND : angle 1.67555 ( 32) hydrogen bonds : bond 0.04938 ( 1062) hydrogen bonds : angle 4.48778 ( 3072) metal coordination : bond 0.00070 ( 2) link_BETA1-4 : bond 0.00450 ( 18) link_BETA1-4 : angle 1.86436 ( 54) link_NAG-ASN : bond 0.01136 ( 26) link_NAG-ASN : angle 5.18268 ( 78) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 234 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 HIS cc_start: 0.6653 (t-170) cc_final: 0.6327 (t-90) REVERT: A 583 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6981 (m-10) REVERT: B 26 LYS cc_start: 0.7912 (tttt) cc_final: 0.7566 (mtpp) REVERT: B 62 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7169 (ptm) REVERT: B 83 TYR cc_start: 0.7816 (m-80) cc_final: 0.7457 (m-80) REVERT: B 102 GLN cc_start: 0.8658 (tp40) cc_final: 0.8060 (pm20) REVERT: B 332 MET cc_start: 0.8523 (ptm) cc_final: 0.8274 (ppp) REVERT: B 345 HIS cc_start: 0.7197 (t-170) cc_final: 0.6636 (m170) REVERT: B 556 ASN cc_start: 0.8821 (t0) cc_final: 0.8305 (t0) REVERT: B 651 MET cc_start: 0.9446 (mmm) cc_final: 0.9173 (mmt) REVERT: B 706 MET cc_start: 0.8860 (ttp) cc_final: 0.8539 (ttm) REVERT: B 713 ASP cc_start: 0.8924 (m-30) cc_final: 0.8685 (m-30) REVERT: E 464 PHE cc_start: 0.6211 (m-80) cc_final: 0.5165 (t80) REVERT: C 583 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6976 (m-10) REVERT: D 26 LYS cc_start: 0.7914 (tttt) cc_final: 0.7559 (mtpp) REVERT: D 62 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.7172 (ptm) REVERT: D 83 TYR cc_start: 0.7818 (m-80) cc_final: 0.7457 (m-80) REVERT: D 102 GLN cc_start: 0.8678 (tp40) cc_final: 0.8066 (pm20) REVERT: D 332 MET cc_start: 0.8526 (ptm) cc_final: 0.8274 (ppp) REVERT: D 345 HIS cc_start: 0.7192 (t-170) cc_final: 0.6633 (m90) REVERT: D 556 ASN cc_start: 0.8811 (t0) cc_final: 0.8298 (t0) REVERT: D 651 MET cc_start: 0.9452 (mmm) cc_final: 0.9176 (mmt) REVERT: D 706 MET cc_start: 0.8862 (ttp) cc_final: 0.8541 (ttm) REVERT: D 713 ASP cc_start: 0.8930 (m-30) cc_final: 0.8692 (m-30) REVERT: F 464 PHE cc_start: 0.6186 (m-80) cc_final: 0.5330 (t80) outliers start: 76 outliers final: 61 residues processed: 298 average time/residue: 0.4910 time to fit residues: 175.6917 Evaluate side-chains 289 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 224 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 516 LYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 583 TYR Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 743 LEU Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 488 CYS Chi-restraints excluded: chain E residue 501 ASN Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 516 LYS Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 585 VAL Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 686 THR Chi-restraints excluded: chain D residue 692 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 763 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 382 VAL Chi-restraints excluded: chain F residue 430 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 488 CYS Chi-restraints excluded: chain F residue 501 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 176 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 187 optimal weight: 6.9990 chunk 190 optimal weight: 0.0670 chunk 206 optimal weight: 0.9990 chunk 240 optimal weight: 0.8980 chunk 197 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 252 optimal weight: 7.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 435 ASN ** C 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN C 435 ASN F 501 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.157084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.099364 restraints weight = 43868.691| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.31 r_work: 0.3207 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 26084 Z= 0.199 Angle : 0.917 59.200 35578 Z= 0.502 Chirality : 0.048 0.438 3980 Planarity : 0.005 0.132 4452 Dihedral : 5.884 57.002 4254 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.72 % Favored : 94.02 % Rotamer: Outliers : 2.88 % Allowed : 23.65 % Favored : 73.47 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.15), residues: 3060 helix: 0.20 (0.13), residues: 1714 sheet: 0.04 (0.45), residues: 126 loop : -1.51 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 306 TYR 0.020 0.002 TYR A 488 PHE 0.029 0.001 PHE D 72 TRP 0.025 0.001 TRP F 436 HIS 0.011 0.001 HIS C 108 Details of bonding type rmsd covalent geometry : bond 0.00441 (26022) covalent geometry : angle 0.87764 (35414) SS BOND : bond 0.01751 ( 16) SS BOND : angle 3.44130 ( 32) hydrogen bonds : bond 0.04772 ( 1062) hydrogen bonds : angle 4.48768 ( 3072) metal coordination : bond 0.00147 ( 2) link_BETA1-4 : bond 0.00516 ( 18) link_BETA1-4 : angle 1.87346 ( 54) link_NAG-ASN : bond 0.01126 ( 26) link_NAG-ASN : angle 5.17843 ( 78) =============================================================================== Job complete usr+sys time: 10607.70 seconds wall clock time: 180 minutes 22.48 seconds (10822.48 seconds total)