Starting phenix.real_space_refine on Sun Sep 13 07:59:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6jp8_9867/09_2026/6jp8_9867.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jp8_9867/09_2026/6jp8_9867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6jp8_9867/09_2026/6jp8_9867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jp8_9867/09_2026/6jp8_9867.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6jp8_9867/09_2026/6jp8_9867.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6jp8_9867/09_2026/6jp8_9867.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jp8_9867/09_2026/6jp8_9867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jp8_9867/09_2026/6jp8_9867.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 S 126 5.16 5 C 14087 2.51 5 N 3587 2.21 5 O 3996 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21801 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 Chain: "B" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 710 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 91} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1367 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 165} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 10219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1274, 10219 Classifications: {'peptide': 1274} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 38, 'TRANS': 1235} Chain breaks: 6 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "D" 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 chiralities: 2 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 chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 chiralities: 2 Chain: "L" 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 chiralities: 3 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' CA': 2, 'C8U': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 102 Unusual residues: {'ETA': 1, 'NAG': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.91, per 1000 atoms: 0.27 Number of scatterers: 21801 At special positions: 0 Unit cell: (170.196, 182.197, 165.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 126 16.00 F 3 9.00 O 3996 8.00 N 3587 7.00 C 14087 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.05 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.91 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.40 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.75 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.03 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.77 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.27 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.02 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=1.57 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " distance=2.02 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 Atom "HETATM21715 O5 NAG F1104 .*. O " rejected from bonding due to valence issues. Atom "HETATM21743 O5 NAG F1114 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-3 " NAG D 1 " - " NAG D 2 " " NAG K 1 " - " NAG K 2 " " NAG L 2 " - " NAG L 3 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG F1104 " - " ASN F 326 " " NAG F1107 " - " ASN F 891 " " NAG F1114 " - " ASN F 92 " " NAG F1115 " - " ASN F 606 " " NAG F1120 " - " ASN F 784 " " NAG F1121 " - " ASN F1001 " " NAG F1122 " - " ASN F 988 " " NAG G 1 " - " ASN F 615 " " NAG H 1 " - " ASN F 186 " " NAG I 1 " - " ASN F 470 " " NAG J 1 " - " ASN F 898 " " NAG K 1 " - " ASN F 678 " " NAG L 1 " - " ASN F 827 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.3 seconds 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5110 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 20 sheets defined 52.9% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'E' and resid 7 through 27 removed outlier: 3.948A pdb=" N THR E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET E 24 " --> pdb=" O ILE E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 128 removed outlier: 3.961A pdb=" N PHE E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE E 123 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 165 removed outlier: 3.804A pdb=" N ALA E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET E 142 " --> pdb=" O ARG E 138 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE E 143 " --> pdb=" O PRO E 139 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER E 154 " --> pdb=" O CYS E 150 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN E 160 " --> pdb=" O GLU E 156 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER E 161 " --> pdb=" O VAL E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 202 removed outlier: 3.776A pdb=" N ALA E 185 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE E 197 " --> pdb=" O PHE E 193 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 95 removed outlier: 3.600A pdb=" N ARG B 82 " --> pdb=" O HIS B 78 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 83 " --> pdb=" O MET B 79 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 88 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 171 removed outlier: 3.991A pdb=" N ARG B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU B 170 " --> pdb=" O ASP B 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 304 removed outlier: 3.532A pdb=" N ASP C 291 " --> pdb=" O TYR C 287 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 297 " --> pdb=" O MET C 293 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 300 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N HIS C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 357 removed outlier: 3.723A pdb=" N VAL C 347 " --> pdb=" O SER C 343 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU C 350 " --> pdb=" O GLU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.567A pdb=" N SER C 378 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 402 removed outlier: 4.026A pdb=" N LEU C 397 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN C 398 " --> pdb=" O PRO C 394 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 410 removed outlier: 3.761A pdb=" N LYS C 410 " --> pdb=" O SER C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 407 through 410' Processing helix chain 'C' and resid 411 through 425 removed outlier: 4.041A pdb=" N GLN C 415 " --> pdb=" O HIS C 411 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 417 " --> pdb=" O ASN C 413 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA C 418 " --> pdb=" O VAL C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 438 through 458 removed outlier: 3.549A pdb=" N ALA C 442 " --> pdb=" O GLN C 438 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS C 445 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.585A pdb=" N GLU A 49 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 71 removed outlier: 3.864A pdb=" N THR A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 57 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 86 removed outlier: 3.544A pdb=" N LEU A 84 " --> pdb=" O ASN A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 103 removed outlier: 3.644A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 115 Processing helix chain 'A' and resid 120 through 143 removed outlier: 3.914A pdb=" N VAL A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.718A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 182 through 192 removed outlier: 3.745A pdb=" N LEU A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN A 187 " --> pdb=" O GLN A 183 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 219 removed outlier: 3.696A pdb=" N ALA A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 Processing helix chain 'A' and resid 293 through 306 removed outlier: 3.636A pdb=" N VAL A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 321 removed outlier: 3.605A pdb=" N THR A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 345 removed outlier: 4.437A pdb=" N ARG A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ALA A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 372 removed outlier: 3.889A pdb=" N LEU A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG A 354 " --> pdb=" O PHE A 350 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU A 355 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 360 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TRP A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 430 removed outlier: 3.670A pdb=" N TRP A 423 " --> pdb=" O ARG A 419 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP A 427 " --> pdb=" O TRP A 423 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 428 " --> pdb=" O LYS A 424 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 429 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 430 " --> pdb=" O HIS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 437 removed outlier: 3.513A pdb=" N LEU A 437 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 451 removed outlier: 3.794A pdb=" N LEU A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 486 removed outlier: 3.752A pdb=" N ASN A 468 " --> pdb=" O GLN A 464 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.584A pdb=" N PHE A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 515 removed outlier: 3.571A pdb=" N PHE A 499 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N CYS A 501 " --> pdb=" O ASN A 497 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 503 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 509 " --> pdb=" O CYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 removed outlier: 3.927A pdb=" N VAL A 526 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 522 through 527' Processing helix chain 'A' and resid 530 through 542 removed outlier: 3.658A pdb=" N LEU A 535 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS A 537 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 538 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 539 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 540 " --> pdb=" O LYS A 537 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP A 542 " --> pdb=" O THR A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 554 removed outlier: 3.555A pdb=" N VAL A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 582 removed outlier: 3.510A pdb=" N ALA A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 613 Processing helix chain 'A' and resid 615 through 626 removed outlier: 3.650A pdb=" N VAL A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 636 Processing helix chain 'A' and resid 637 through 663 removed outlier: 4.159A pdb=" N PHE A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU A 657 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 658 " --> pdb=" O ASN A 654 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 660 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A 662 " --> pdb=" O ALA A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 674 Processing helix chain 'A' and resid 674 through 679 removed outlier: 3.728A pdb=" N ALA A 678 " --> pdb=" O GLN A 674 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 674 through 679' Processing helix chain 'A' and resid 681 through 686 removed outlier: 3.711A pdb=" N LYS A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 795 removed outlier: 3.628A pdb=" N ILE A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 818 removed outlier: 3.643A pdb=" N LEU A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 808 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 811 " --> pdb=" O LEU A 807 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 832 removed outlier: 3.542A pdb=" N ILE A 831 " --> pdb=" O VAL A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 852 removed outlier: 3.821A pdb=" N VAL A 842 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 883 Processing helix chain 'A' and resid 893 through 897 Processing helix chain 'A' and resid 898 through 905 removed outlier: 3.733A pdb=" N LEU A 902 " --> pdb=" O LEU A 899 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG A 903 " --> pdb=" O ARG A 900 " (cutoff:3.500A) Proline residue: A 904 - end of helix Processing helix chain 'A' and resid 906 through 911 removed outlier: 3.673A pdb=" N ARG A 910 " --> pdb=" O ARG A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 951 removed outlier: 3.727A pdb=" N HIS A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 917 " --> pdb=" O GLY A 913 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 918 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 928 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN A 930 " --> pdb=" O ARG A 926 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE A 931 " --> pdb=" O THR A 927 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 940 " --> pdb=" O THR A 936 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 951 " --> pdb=" O VAL A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 979 No H-bonds generated for 'chain 'A' and resid 977 through 979' Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1015 through 1025 Processing helix chain 'A' and resid 1038 through 1040 No H-bonds generated for 'chain 'A' and resid 1038 through 1040' Processing helix chain 'A' and resid 1041 through 1052 removed outlier: 3.716A pdb=" N PHE A1045 " --> pdb=" O MET A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1070 removed outlier: 4.239A pdb=" N PHE A1063 " --> pdb=" O ILE A1059 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A1064 " --> pdb=" O PHE A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1073 No H-bonds generated for 'chain 'A' and resid 1071 through 1073' Processing helix chain 'A' and resid 1082 through 1095 removed outlier: 3.593A pdb=" N CYS A1088 " --> pdb=" O ASN A1084 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN A1090 " --> pdb=" O ARG A1086 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR A1091 " --> pdb=" O GLN A1087 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A1092 " --> pdb=" O CYS A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1116 removed outlier: 4.054A pdb=" N VAL A1114 " --> pdb=" O GLN A1110 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A1115 " --> pdb=" O VAL A1111 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A1116 " --> pdb=" O TRP A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1137 removed outlier: 3.568A pdb=" N PHE A1125 " --> pdb=" O GLU A1121 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET A1129 " --> pdb=" O PHE A1125 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A1130 " --> pdb=" O ALA A1126 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1148 removed outlier: 3.594A pdb=" N HIS A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1172 removed outlier: 3.554A pdb=" N LEU A1153 " --> pdb=" O ILE A1149 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN A1154 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1179 removed outlier: 4.106A pdb=" N PHE A1178 " --> pdb=" O ALA A1174 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY A1179 " --> pdb=" O ARG A1175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1174 through 1179' Processing helix chain 'A' and resid 1180 through 1206 removed outlier: 3.583A pdb=" N VAL A1184 " --> pdb=" O ASP A1180 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A1186 " --> pdb=" O TRP A1182 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A1196 " --> pdb=" O GLY A1192 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A1197 " --> pdb=" O SER A1193 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A1204 " --> pdb=" O SER A1200 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A1206 " --> pdb=" O ILE A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1242 removed outlier: 3.958A pdb=" N VAL A1240 " --> pdb=" O ARG A1236 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A1242 " --> pdb=" O PHE A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1249 removed outlier: 3.703A pdb=" N ARG A1249 " --> pdb=" O LEU A1246 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1267 removed outlier: 3.589A pdb=" N SER A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1290 removed outlier: 4.272A pdb=" N ALA A1271 " --> pdb=" O LEU A1267 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1322 Processing helix chain 'A' and resid 1324 through 1331 Processing helix chain 'A' and resid 1356 through 1383 removed outlier: 3.616A pdb=" N ASP A1382 " --> pdb=" O ALA A1378 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1388 Processing helix chain 'A' and resid 1395 through 1408 removed outlier: 3.971A pdb=" N LEU A1399 " --> pdb=" O GLY A1395 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A1404 " --> pdb=" O ASP A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1422 removed outlier: 3.858A pdb=" N ASP A1421 " --> pdb=" O LYS A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1451 Processing helix chain 'A' and resid 1463 through 1472 removed outlier: 3.611A pdb=" N LEU A1467 " --> pdb=" O PHE A1463 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N PHE A1468 " --> pdb=" O ASN A1464 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A1469 " --> pdb=" O ALA A1465 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A1471 " --> pdb=" O LEU A1467 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 38 Processing helix chain 'F' and resid 41 through 53 removed outlier: 3.800A pdb=" N GLY F 53 " --> pdb=" O LYS F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 65 removed outlier: 3.652A pdb=" N TYR F 64 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN F 65 " --> pdb=" O TYR F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 109 removed outlier: 3.725A pdb=" N SER F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 188 removed outlier: 3.919A pdb=" N GLU F 184 " --> pdb=" O ILE F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 202 removed outlier: 3.604A pdb=" N ARG F 199 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU F 201 " --> pdb=" O LYS F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 251 removed outlier: 3.862A pdb=" N GLY F 249 " --> pdb=" O TRP F 245 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA F 251 " --> pdb=" O ILE F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 267 Processing helix chain 'F' and resid 268 through 284 removed outlier: 3.616A pdb=" N ARG F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER F 279 " --> pdb=" O ARG F 275 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 324 Processing helix chain 'F' and resid 334 through 347 Processing helix chain 'F' and resid 371 through 379 removed outlier: 3.827A pdb=" N PHE F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS F 377 " --> pdb=" O GLU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 408 Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 428 through 433 Processing helix chain 'F' and resid 433 through 438 Processing helix chain 'F' and resid 439 through 444 removed outlier: 3.682A pdb=" N LYS F 442 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 Processing helix chain 'F' and resid 542 through 546 removed outlier: 3.843A pdb=" N ARG F 546 " --> pdb=" O LEU F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 562 through 567 removed outlier: 3.501A pdb=" N GLU F 567 " --> pdb=" O PHE F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 580 Processing helix chain 'F' and resid 640 through 647 Processing helix chain 'F' and resid 652 through 656 removed outlier: 4.022A pdb=" N PHE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 693 removed outlier: 3.686A pdb=" N PHE F 689 " --> pdb=" O ASN F 685 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE F 690 " --> pdb=" O PHE F 686 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP F 691 " --> pdb=" O ASN F 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 713 removed outlier: 4.022A pdb=" N ILE F 705 " --> pdb=" O ASN F 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 713 through 722 removed outlier: 3.839A pdb=" N GLU F 717 " --> pdb=" O GLY F 713 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU F 718 " --> pdb=" O PHE F 714 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL F 719 " --> pdb=" O THR F 715 " (cutoff:3.500A) Processing helix chain 'F' and resid 750 through 754 removed outlier: 3.519A pdb=" N GLU F 753 " --> pdb=" O GLU F 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 764 through 773 removed outlier: 3.650A pdb=" N LYS F 768 " --> pdb=" O ASP F 764 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 771 " --> pdb=" O TYR F 767 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP F 772 " --> pdb=" O LYS F 768 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN F 773 " --> pdb=" O ARG F 769 " (cutoff:3.500A) Processing helix chain 'F' and resid 820 through 830 removed outlier: 3.507A pdb=" N GLU F 826 " --> pdb=" O ASN F 822 " (cutoff:3.500A) Processing helix chain 'F' and resid 877 through 881 Processing helix chain 'F' and resid 882 through 892 removed outlier: 3.619A pdb=" N MET F 886 " --> pdb=" O ASP F 882 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN F 891 " --> pdb=" O ARG F 887 " (cutoff:3.500A) Processing helix chain 'F' and resid 1024 through 1027 Processing helix chain 'F' and resid 1045 through 1050 removed outlier: 3.752A pdb=" N MET F1049 " --> pdb=" O ASP F1045 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 48 through 50 removed outlier: 3.681A pdb=" N CYS E 57 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASN E 79 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 156 through 160 removed outlier: 6.459A pdb=" N ARG B 148 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE B 136 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 103 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA B 104 " --> pdb=" O VAL C 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 309 through 313 removed outlier: 6.374A pdb=" N SER C 310 " --> pdb=" O ALA C 365 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASP C 367 " --> pdb=" O SER C 310 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR C 312 " --> pdb=" O ASP C 367 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU C 279 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 228 removed outlier: 3.969A pdb=" N THR A 225 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 262 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 260 " --> pdb=" O TYR A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 955 through 957 Processing sheet with id=AA6, first strand: chain 'A' and resid 971 through 975 Processing sheet with id=AA7, first strand: chain 'A' and resid 1416 through 1417 removed outlier: 3.797A pdb=" N VAL A1461 " --> pdb=" O ILE A1417 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 68 through 72 Processing sheet with id=AA9, first strand: chain 'F' and resid 124 through 125 removed outlier: 6.028A pdb=" N VAL F 124 " --> pdb=" O GLN F 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.993A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY F 488 " --> pdb=" O VAL F 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.993A pdb=" N TYR F 127 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY F 488 " --> pdb=" O VAL F 468 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 300 through 302 removed outlier: 5.987A pdb=" N LYS F 254 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ASN F 292 " --> pdb=" O LYS F 254 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N MET F 256 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ALA F 294 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE F 258 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE F 296 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL F 260 " --> pdb=" O PHE F 296 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE F 359 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS F 358 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N PHE F 387 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE F 360 " --> pdb=" O PHE F 387 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N PHE F 389 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU F 362 " --> pdb=" O PHE F 389 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL F 391 " --> pdb=" O LEU F 362 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR F 364 " --> pdb=" O VAL F 391 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL F 386 " --> pdb=" O TYR F 411 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N TYR F 413 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR F 388 " --> pdb=" O TYR F 413 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILE F 415 " --> pdb=" O THR F 388 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER F 390 " --> pdb=" O ILE F 415 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 523 through 525 removed outlier: 3.660A pdb=" N LEU F 525 " --> pdb=" O ALA F 516 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 661 through 662 Processing sheet with id=AB6, first strand: chain 'F' and resid 732 through 734 removed outlier: 3.564A pdb=" N ALA F 734 " --> pdb=" O LYS F 818 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 732 through 734 removed outlier: 3.564A pdb=" N ALA F 734 " --> pdb=" O LYS F 818 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 803 through 804 Processing sheet with id=AB9, first strand: chain 'F' and resid 862 through 865 removed outlier: 3.618A pdb=" N MET F 864 " --> pdb=" O ILE F 855 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 896 through 907 removed outlier: 3.619A pdb=" N GLN F 983 " --> pdb=" O ASN F 898 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLN F 904 " --> pdb=" O CYS F 977 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N CYS F 977 " --> pdb=" O GLN F 904 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL F 906 " --> pdb=" O GLN F 975 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN F 975 " --> pdb=" O VAL F 906 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 997 through 998 916 hydrogen bonds defined for protein. 2579 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: 4.77 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3540 1.30 - 1.44: 6130 1.44 - 1.57: 12415 1.57 - 1.70: 4 1.70 - 1.84: 194 Bond restraints: 22283 Sorted by residual: bond pdb=" N09 C8U A1901 " pdb=" O11 C8U A1901 " ideal model delta sigma weight residual 1.220 1.400 -0.180 2.00e-02 2.50e+03 8.06e+01 bond pdb=" C02 C8U A1901 " pdb=" C03 C8U A1901 " ideal model delta sigma weight residual 1.351 1.521 -0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" C05 C8U A1901 " pdb=" C06 C8U A1901 " ideal model delta sigma weight residual 1.364 1.524 -0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" C ALA F 665 " pdb=" N PRO F 666 " ideal model delta sigma weight residual 1.334 1.206 0.128 2.34e-02 1.83e+03 2.99e+01 bond pdb=" C ALA F 780 " pdb=" N PRO F 781 " ideal model delta sigma weight residual 1.330 1.389 -0.059 1.22e-02 6.72e+03 2.32e+01 ... (remaining 22278 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 28705 3.06 - 6.11: 1278 6.11 - 9.17: 185 9.17 - 12.22: 35 12.22 - 15.28: 14 Bond angle restraints: 30217 Sorted by residual: angle pdb=" N HIS F 867 " pdb=" CA HIS F 867 " pdb=" C HIS F 867 " ideal model delta sigma weight residual 111.28 122.21 -10.93 1.09e+00 8.42e-01 1.01e+02 angle pdb=" N LYS F 478 " pdb=" CA LYS F 478 " pdb=" C LYS F 478 " ideal model delta sigma weight residual 111.28 121.91 -10.63 1.09e+00 8.42e-01 9.51e+01 angle pdb=" N ALA A 450 " pdb=" CA ALA A 450 " pdb=" C ALA A 450 " ideal model delta sigma weight residual 111.28 121.84 -10.56 1.09e+00 8.42e-01 9.39e+01 angle pdb=" N LEU A 217 " pdb=" CA LEU A 217 " pdb=" C LEU A 217 " ideal model delta sigma weight residual 111.36 120.71 -9.35 1.09e+00 8.42e-01 7.36e+01 angle pdb=" N ARG A 41 " pdb=" CA ARG A 41 " pdb=" C ARG A 41 " ideal model delta sigma weight residual 111.07 120.11 -9.04 1.07e+00 8.73e-01 7.15e+01 ... (remaining 30212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.02: 12367 23.02 - 46.04: 606 46.04 - 69.06: 108 69.06 - 92.08: 21 92.08 - 115.10: 1 Dihedral angle restraints: 13103 sinusoidal: 5204 harmonic: 7899 Sorted by residual: dihedral pdb=" CB CYS F 406 " pdb=" SG CYS F 406 " pdb=" SG CYS F1074 " pdb=" CB CYS F1074 " ideal model delta sinusoidal sigma weight residual -86.00 0.03 -86.03 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS F 907 " pdb=" SG CYS F 907 " pdb=" SG CYS F 977 " pdb=" CB CYS F 977 " ideal model delta sinusoidal sigma weight residual 93.00 174.04 -81.04 1 1.00e+01 1.00e-02 8.11e+01 dihedral pdb=" CB CYS F 844 " pdb=" SG CYS F 844 " pdb=" SG CYS F 853 " pdb=" CB CYS F 853 " ideal model delta sinusoidal sigma weight residual -86.00 -161.98 75.98 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 13100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.765: 3474 0.765 - 1.531: 2 1.531 - 2.296: 0 2.296 - 3.062: 1 3.062 - 3.827: 1 Chirality restraints: 3478 Sorted by residual: chirality pdb=" C1 NAG L 3 " pdb=" O3 NAG L 2 " pdb=" C2 NAG L 3 " pdb=" O5 NAG L 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-02 2.50e+03 1.04e+03 chirality pdb=" C1 NAG F1120 " pdb=" ND2 ASN F 784 " pdb=" C2 NAG F1120 " pdb=" O5 NAG F1120 " both_signs ideal model delta sigma weight residual False -2.40 1.43 -3.83 2.00e-01 2.50e+01 3.66e+02 chirality pdb=" C1 NAG D 2 " pdb=" O3 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-02 2.50e+03 1.94e+02 ... (remaining 3475 not shown) Planarity restraints: 3807 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " 0.346 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG L 1 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " 0.104 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " 0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.344 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG D 1 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " -0.116 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.532 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.153 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F1104 " -0.315 2.00e-02 2.50e+03 2.67e-01 8.88e+02 pdb=" C7 NAG F1104 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG F1104 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG F1104 " 0.462 2.00e-02 2.50e+03 pdb=" O7 NAG F1104 " -0.042 2.00e-02 2.50e+03 ... (remaining 3804 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 114 2.48 - 3.09: 14212 3.09 - 3.69: 32808 3.69 - 4.30: 48271 4.30 - 4.90: 77984 Nonbonded interactions: 173389 Sorted by model distance: nonbonded pdb=" O ARG F 846 " pdb=" ND2 ASN F 847 " model vdw 1.877 3.120 nonbonded pdb=" O ASN F 480 " pdb=" ND2 ASN F 480 " model vdw 1.920 3.120 nonbonded pdb=" O LYS F 845 " pdb=" OG SER F 848 " model vdw 1.973 3.040 nonbonded pdb=" OD1 ASN F 891 " pdb=" O5 NAG F1107 " model vdw 2.082 3.040 nonbonded pdb=" CB PHE A 656 " pdb=" ND2 ASN A1058 " model vdw 2.134 3.520 ... (remaining 173384 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'K' } ncs_group { reference = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.070 Set stop_for_unknowns flag: 0.010 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: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.200 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:7.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5194 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 : 0.018 0.881 22320 Z= 0.935 Angle : 1.727 58.012 30312 Z= 0.939 Chirality : 0.124 3.827 3478 Planarity : 0.014 0.300 3794 Dihedral : 14.012 115.095 7954 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 25.96 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.22 % Favored : 92.33 % Rotamer: Outliers : 6.07 % Allowed : 7.50 % Favored : 86.44 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 1.82 % 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: -4.05 (0.14), residues: 2659 helix: -2.98 (0.11), residues: 1295 sheet: -1.24 (0.35), residues: 212 loop : -2.46 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.002 ARG A 594 TYR 0.071 0.005 TYR A 627 PHE 0.047 0.005 PHE A1289 TRP 0.044 0.005 TRP E 32 HIS 0.027 0.003 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.01312 / 0.63 (22283) covalent geometry : angle 1.47551 / 0.87 (30217) SS BOND : bond 0.41562 / 20.79 ( 13) SS BOND : angle 18.83146 / 11.89 ( 26) hydrogen bonds : bond 0.29343 / 19.36 ( 896) hydrogen bonds : angle 9.78413 / 6.79 ( 2579) Misc. bond : bond 0.58128 / 30.59 ( 1) link_BETA1-3 : bond 0.00268 / 0.14 ( 3) link_BETA1-3 : angle 11.54409 / 6.67 ( 9) link_BETA1-4 : bond 0.04656 / 1.87 ( 7) link_BETA1-4 : angle 15.31694 / 8.27 ( 21) link_NAG-ASN : bond 0.22619 / 12.47 ( 13) link_NAG-ASN : angle 15.41707 / 8.84 ( 39) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 434 time to evaluate : 0.732 Fit side-chains Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 119 ILE cc_start: 0.3930 (OUTLIER) cc_final: 0.3683 (tt) REVERT: E 133 ARG cc_start: 0.5603 (pmm-80) cc_final: 0.5198 (ptm160) REVERT: E 134 ASP cc_start: 0.6399 (OUTLIER) cc_final: 0.5264 (t0) REVERT: C 274 MET cc_start: -0.0449 (mmm) cc_final: -0.0901 (mpp) REVERT: A 164 LEU cc_start: 0.5566 (mp) cc_final: 0.5346 (mt) REVERT: A 988 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7110 (ptt180) REVERT: A 1005 MET cc_start: 0.8240 (tpt) cc_final: 0.8038 (tpt) REVERT: A 1014 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7811 (tp30) REVERT: A 1188 LEU cc_start: 0.7332 (tt) cc_final: 0.7105 (mt) REVERT: A 1318 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7174 (ttp-170) REVERT: F 62 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6498 (tt0) REVERT: F 124 VAL cc_start: 0.7048 (t) cc_final: 0.6726 (m) REVERT: F 148 LYS cc_start: 0.6548 (mppt) cc_final: 0.6065 (mttm) REVERT: F 202 ASP cc_start: 0.5555 (t0) cc_final: 0.4822 (m-30) REVERT: F 227 ASP cc_start: 0.5849 (m-30) cc_final: 0.5422 (m-30) REVERT: F 237 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7174 (mp) REVERT: F 271 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7256 (tp) REVERT: F 281 MET cc_start: 0.7880 (tpp) cc_final: 0.7606 (tpt) REVERT: F 283 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6888 (mm-30) REVERT: F 307 GLN cc_start: 0.6630 (mt0) cc_final: 0.6372 (mp10) REVERT: F 330 LYS cc_start: 0.6779 (tttm) cc_final: 0.6532 (ttmt) REVERT: F 361 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7609 (ptp) REVERT: F 382 LYS cc_start: 0.6747 (OUTLIER) cc_final: 0.6372 (mttt) REVERT: F 436 MET cc_start: 0.7770 (ttp) cc_final: 0.7467 (ttp) REVERT: F 590 PHE cc_start: 0.8202 (p90) cc_final: 0.7976 (p90) REVERT: F 593 LEU cc_start: 0.7078 (OUTLIER) cc_final: 0.6849 (pp) REVERT: F 635 LYS cc_start: 0.6041 (ttpt) cc_final: 0.5798 (ttpt) REVERT: F 657 GLU cc_start: 0.5287 (OUTLIER) cc_final: 0.4924 (mm-30) REVERT: F 689 PHE cc_start: 0.5774 (t80) cc_final: 0.5546 (m-80) REVERT: F 793 SER cc_start: 0.5342 (OUTLIER) cc_final: 0.4728 (p) REVERT: F 990 SER cc_start: 0.5934 (OUTLIER) cc_final: 0.4717 (m) REVERT: F 1034 LEU cc_start: 0.6721 (tt) cc_final: 0.6362 (pt) REVERT: F 1055 TYR cc_start: 0.8208 (t80) cc_final: 0.7850 (t80) outliers start: 140 outliers final: 21 residues processed: 537 average time/residue: 0.5687 time to fit residues: 352.9302 Evaluate side-chains 282 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 134 ASP Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 988 ARG Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1014 GLU Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 382 LYS Chi-restraints excluded: chain F residue 441 ASP Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 793 SER Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 990 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 38 HIS E 50 HIS ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN A 183 GLN A 274 HIS A 327 ASN A 445 ASN A 455 ASN A 579 GLN A 869 ASN A 930 ASN ** A 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 ASN ** A1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 ASN A1138 GLN A1287 GLN A1464 ASN F 56 GLN F 108 GLN F 228 ASN F 297 ASN F 308 HIS F 350 ASN F 395 ASN F 450 ASN ** F 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 520 ASN ** F 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 697 ASN F 726 GLN F 773 ASN ** F 888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1065 ASN ** F1066 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.234975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.192908 restraints weight = 38114.755| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 5.90 r_work: 0.3550 rms_B_bonded: 5.35 restraints_weight: 2.0000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22320 Z= 0.170 Angle : 0.854 17.665 30312 Z= 0.419 Chirality : 0.049 0.415 3478 Planarity : 0.006 0.077 3794 Dihedral : 8.245 85.236 2989 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.59 % Favored : 95.33 % Rotamer: Outliers : 5.81 % Allowed : 13.95 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.58 (0.15), residues: 2659 helix: -1.46 (0.13), residues: 1299 sheet: -0.87 (0.31), residues: 275 loop : -2.11 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 275 TYR 0.028 0.002 TYR F 629 PHE 0.020 0.002 PHE F 878 TRP 0.023 0.002 TRP A 309 HIS 0.012 0.001 HIS F 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (22283) covalent geometry : angle 0.81720 / 0.41 (30217) SS BOND : bond 0.01160 / 0.61 ( 13) SS BOND : angle 2.49932 / 1.23 ( 26) hydrogen bonds : bond 0.05142 / 3.38 ( 896) hydrogen bonds : angle 5.15423 / 3.55 ( 2579) Misc. bond : bond 0.02397 / 1.26 ( 1) link_BETA1-3 : bond 0.01373 / 0.69 ( 3) link_BETA1-3 : angle 2.17713 / 1.13 ( 9) link_BETA1-4 : bond 0.01879 / 0.75 ( 7) link_BETA1-4 : angle 3.53288 / 1.83 ( 21) link_NAG-ASN : bond 0.01025 / 0.55 ( 13) link_NAG-ASN : angle 6.09529 / 3.70 ( 39) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 304 time to evaluate : 0.784 Fit side-chains Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 MET cc_start: 0.4820 (tpp) cc_final: 0.4574 (mmt) REVERT: E 131 LYS cc_start: 0.4575 (mtmm) cc_final: 0.4273 (ttmm) REVERT: A 51 LYS cc_start: 0.4014 (OUTLIER) cc_final: 0.3045 (tppp) REVERT: A 175 LEU cc_start: 0.6826 (mt) cc_final: 0.6570 (mt) REVERT: A 182 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6192 (tp) REVERT: A 196 LEU cc_start: 0.7643 (mp) cc_final: 0.7378 (mm) REVERT: A 206 MET cc_start: 0.8075 (ttm) cc_final: 0.7752 (mtm) REVERT: A 282 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7782 (tpt) REVERT: A 340 GLU cc_start: 0.5726 (tp30) cc_final: 0.5495 (pp20) REVERT: A 519 MET cc_start: 0.1461 (mpp) cc_final: 0.0890 (mtt) REVERT: A 586 ASP cc_start: 0.7404 (p0) cc_final: 0.7089 (p0) REVERT: A 589 ASP cc_start: 0.7362 (m-30) cc_final: 0.6772 (p0) REVERT: A 620 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8463 (ttp) REVERT: A 894 LYS cc_start: 0.4524 (OUTLIER) cc_final: 0.3958 (tptt) REVERT: A 897 ARG cc_start: 0.5819 (mtp180) cc_final: 0.5383 (mtp-110) REVERT: A 937 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8377 (tp) REVERT: A 983 MET cc_start: 0.8307 (pmm) cc_final: 0.7921 (pmm) REVERT: A 988 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7292 (ptp90) REVERT: A 1058 ASN cc_start: 0.7531 (m110) cc_final: 0.7254 (m-40) REVERT: A 1160 ILE cc_start: 0.7215 (mt) cc_final: 0.6849 (pt) REVERT: A 1188 LEU cc_start: 0.8158 (tt) cc_final: 0.7305 (mt) REVERT: A 1235 PHE cc_start: 0.7497 (m-80) cc_final: 0.7183 (m-80) REVERT: A 1243 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7612 (mt) REVERT: A 1318 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7357 (ttt180) REVERT: A 1348 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6415 (mt-10) REVERT: A 1350 TYR cc_start: 0.7515 (m-10) cc_final: 0.7182 (m-80) REVERT: A 1384 PHE cc_start: 0.5927 (t80) cc_final: 0.5670 (t80) REVERT: A 1475 LEU cc_start: 0.2177 (OUTLIER) cc_final: 0.1837 (tp) REVERT: F 45 VAL cc_start: 0.6988 (p) cc_final: 0.6649 (t) REVERT: F 61 TYR cc_start: 0.7444 (m-80) cc_final: 0.7233 (m-80) REVERT: F 62 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6236 (tt0) REVERT: F 73 ASN cc_start: 0.7820 (m-40) cc_final: 0.7548 (m110) REVERT: F 148 LYS cc_start: 0.6819 (mppt) cc_final: 0.6289 (mttm) REVERT: F 163 TYR cc_start: 0.7947 (m-80) cc_final: 0.7729 (m-80) REVERT: F 202 ASP cc_start: 0.6050 (t0) cc_final: 0.5156 (m-30) REVERT: F 227 ASP cc_start: 0.6271 (m-30) cc_final: 0.5855 (m-30) REVERT: F 237 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7728 (mp) REVERT: F 302 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7555 (p0) REVERT: F 307 GLN cc_start: 0.6860 (mt0) cc_final: 0.6549 (mp10) REVERT: F 361 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7049 (mtt) REVERT: F 372 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6535 (mp10) REVERT: F 442 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6767 (mtmm) REVERT: F 657 GLU cc_start: 0.5159 (OUTLIER) cc_final: 0.4853 (mm-30) REVERT: F 688 GLU cc_start: 0.6583 (tt0) cc_final: 0.6225 (tp30) REVERT: F 689 PHE cc_start: 0.5662 (t80) cc_final: 0.5411 (t80) outliers start: 134 outliers final: 36 residues processed: 398 average time/residue: 0.4762 time to fit residues: 224.4120 Evaluate side-chains 300 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 620 MET Chi-restraints excluded: chain A residue 894 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 988 ARG Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1253 VAL Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1348 GLU Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 302 ASP Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 372 GLN Chi-restraints excluded: chain F residue 391 VAL Chi-restraints excluded: chain F residue 441 ASP Chi-restraints excluded: chain F residue 442 LYS Chi-restraints excluded: chain F residue 498 ASP Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 585 SER Chi-restraints excluded: chain F residue 657 GLU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 797 VAL Chi-restraints excluded: chain F residue 849 ASP Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 36 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 chunk 126 optimal weight: 0.0770 chunk 69 optimal weight: 3.9990 chunk 177 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 169 optimal weight: 9.9990 chunk 230 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A 455 ASN ** A 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1027 ASN A1183 ASN F 160 GLN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 355 ASN F 357 ASN F 511 ASN F 570 ASN F 679 ASN F 687 ASN F1013 ASN F1015 ASN F1066 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.231354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.189086 restraints weight = 36320.237| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 5.40 r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4032 r_free = 0.4032 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4032 r_free = 0.4032 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22320 Z= 0.148 Angle : 0.739 17.367 30312 Z= 0.366 Chirality : 0.047 0.469 3478 Planarity : 0.005 0.067 3794 Dihedral : 7.076 87.069 2958 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.81 % Rotamer: Outliers : 4.94 % Allowed : 17.16 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.88 (0.15), residues: 2659 helix: -0.73 (0.14), residues: 1308 sheet: -0.74 (0.32), residues: 255 loop : -1.91 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1318 TYR 0.023 0.002 TYR F 762 PHE 0.024 0.002 PHE F 590 TRP 0.018 0.002 TRP A 309 HIS 0.013 0.002 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (22283) covalent geometry : angle 0.71342 / 0.36 (30217) SS BOND : bond 0.00452 / 0.23 ( 13) SS BOND : angle 2.48491 / 1.50 ( 26) hydrogen bonds : bond 0.04759 / 3.13 ( 896) hydrogen bonds : angle 4.66257 / 3.20 ( 2579) Misc. bond : bond 0.00143 / 0.08 ( 1) link_BETA1-3 : bond 0.00894 / 0.45 ( 3) link_BETA1-3 : angle 1.29683 / 0.66 ( 9) link_BETA1-4 : bond 0.00860 / 0.36 ( 7) link_BETA1-4 : angle 2.38674 / 1.24 ( 21) link_NAG-ASN : bond 0.00976 / 0.49 ( 13) link_NAG-ASN : angle 4.77428 / 2.76 ( 39) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 268 time to evaluate : 0.806 Fit side-chains Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 MET cc_start: 0.4486 (tpp) cc_final: 0.4285 (mmt) REVERT: E 133 ARG cc_start: 0.5637 (OUTLIER) cc_final: 0.5271 (mpt-90) REVERT: A 51 LYS cc_start: 0.4330 (OUTLIER) cc_final: 0.3388 (tppp) REVERT: A 182 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6142 (tp) REVERT: A 519 MET cc_start: 0.1996 (mpp) cc_final: 0.1381 (mtt) REVERT: A 983 MET cc_start: 0.7728 (pmm) cc_final: 0.7397 (pmm) REVERT: A 1058 ASN cc_start: 0.6577 (m110) cc_final: 0.6214 (m-40) REVERT: A 1070 GLU cc_start: 0.4881 (tt0) cc_final: 0.4176 (tm-30) REVERT: A 1165 MET cc_start: 0.6861 (ttp) cc_final: 0.6595 (ttp) REVERT: A 1296 ASP cc_start: 0.6476 (OUTLIER) cc_final: 0.6249 (t0) REVERT: A 1318 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7403 (ttt180) REVERT: A 1350 TYR cc_start: 0.7250 (m-10) cc_final: 0.6941 (m-10) REVERT: A 1475 LEU cc_start: 0.2048 (OUTLIER) cc_final: 0.1807 (mp) REVERT: F 42 GLU cc_start: 0.5528 (pp20) cc_final: 0.5201 (mp0) REVERT: F 43 ASP cc_start: 0.5136 (m-30) cc_final: 0.4822 (p0) REVERT: F 163 TYR cc_start: 0.7570 (m-80) cc_final: 0.7327 (m-80) REVERT: F 202 ASP cc_start: 0.6234 (t0) cc_final: 0.5498 (m-30) REVERT: F 237 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7734 (mp) REVERT: F 302 ASP cc_start: 0.7082 (p0) cc_final: 0.6695 (p0) REVERT: F 442 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.7016 (mtmm) REVERT: F 480 ASN cc_start: 0.4711 (OUTLIER) cc_final: 0.4248 (t0) REVERT: F 570 ASN cc_start: 0.6745 (m-40) cc_final: 0.6158 (m110) REVERT: F 1065 ASN cc_start: 0.5372 (t0) cc_final: 0.4856 (t0) outliers start: 114 outliers final: 49 residues processed: 351 average time/residue: 0.4763 time to fit residues: 198.7266 Evaluate side-chains 284 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 226 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1010 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1253 VAL Chi-restraints excluded: chain A residue 1296 ASP Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1366 MET Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 355 ASN Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 442 LYS Chi-restraints excluded: chain F residue 480 ASN Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 585 SER Chi-restraints excluded: chain F residue 589 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 797 VAL Chi-restraints excluded: chain F residue 849 ASP Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 906 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 19 optimal weight: 0.1980 chunk 29 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 202 optimal weight: 0.6980 chunk 213 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 40 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS A 123 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** A 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 ASN A1085 GLN F 350 ASN F 866 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.231788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.187523 restraints weight = 31516.541| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 5.97 r_work: 0.3503 rms_B_bonded: 5.15 restraints_weight: 2.0000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22320 Z= 0.123 Angle : 0.670 15.770 30312 Z= 0.328 Chirality : 0.045 0.431 3478 Planarity : 0.005 0.065 3794 Dihedral : 6.301 86.750 2947 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 4.03 % Allowed : 18.93 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.35 (0.16), residues: 2659 helix: -0.20 (0.14), residues: 1307 sheet: -0.63 (0.31), residues: 266 loop : -1.76 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 275 TYR 0.033 0.001 TYR A1091 PHE 0.030 0.001 PHE F 689 TRP 0.015 0.001 TRP A 309 HIS 0.013 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (22283) covalent geometry : angle 0.64667 / 0.32 (30217) SS BOND : bond 0.00526 / 0.36 ( 13) SS BOND : angle 2.21074 / 1.34 ( 26) hydrogen bonds : bond 0.03900 / 2.56 ( 896) hydrogen bonds : angle 4.43376 / 3.04 ( 2579) Misc. bond : bond 0.00018 / 0.01 ( 1) link_BETA1-3 : bond 0.00926 / 0.46 ( 3) link_BETA1-3 : angle 1.27604 / 0.66 ( 9) link_BETA1-4 : bond 0.00906 / 0.38 ( 7) link_BETA1-4 : angle 2.23294 / 1.18 ( 21) link_NAG-ASN : bond 0.00884 / 0.45 ( 13) link_NAG-ASN : angle 4.27825 / 2.47 ( 39) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 255 time to evaluate : 0.818 Fit side-chains Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 MET cc_start: 0.4914 (tpp) cc_final: 0.4682 (mmt) REVERT: E 133 ARG cc_start: 0.5377 (OUTLIER) cc_final: 0.4852 (mpt-90) REVERT: E 216 MET cc_start: 0.3496 (ptm) cc_final: 0.3172 (tmt) REVERT: A 51 LYS cc_start: 0.4394 (OUTLIER) cc_final: 0.3291 (tppp) REVERT: A 175 LEU cc_start: 0.6714 (OUTLIER) cc_final: 0.6182 (mt) REVERT: A 182 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6252 (tp) REVERT: A 194 LEU cc_start: 0.6450 (mm) cc_final: 0.5860 (mp) REVERT: A 519 MET cc_start: 0.1737 (mpp) cc_final: 0.1061 (mtt) REVERT: A 899 LEU cc_start: 0.6797 (mt) cc_final: 0.6077 (tm) REVERT: A 928 ILE cc_start: 0.5891 (OUTLIER) cc_final: 0.5469 (tp) REVERT: A 965 GLU cc_start: 0.8284 (tt0) cc_final: 0.8079 (tt0) REVERT: A 983 MET cc_start: 0.8275 (pmm) cc_final: 0.8040 (pmm) REVERT: A 1058 ASN cc_start: 0.7226 (m110) cc_final: 0.6911 (m-40) REVERT: A 1070 GLU cc_start: 0.5045 (tt0) cc_final: 0.4216 (tm-30) REVERT: A 1121 GLU cc_start: 0.5699 (mm-30) cc_final: 0.5477 (tm-30) REVERT: A 1165 MET cc_start: 0.7647 (ttp) cc_final: 0.7326 (ttp) REVERT: A 1235 PHE cc_start: 0.7591 (m-80) cc_final: 0.7188 (m-10) REVERT: A 1288 MET cc_start: 0.8085 (mmp) cc_final: 0.7762 (mpt) REVERT: A 1318 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7408 (ttt180) REVERT: A 1350 TYR cc_start: 0.7859 (m-10) cc_final: 0.7495 (m-10) REVERT: A 1387 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6898 (mm) REVERT: A 1475 LEU cc_start: 0.2341 (OUTLIER) cc_final: 0.2090 (mp) REVERT: F 42 GLU cc_start: 0.5683 (pp20) cc_final: 0.5096 (mp0) REVERT: F 61 TYR cc_start: 0.7523 (m-80) cc_final: 0.7100 (m-80) REVERT: F 202 ASP cc_start: 0.6358 (t0) cc_final: 0.5306 (m-30) REVERT: F 271 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8468 (tm) REVERT: F 302 ASP cc_start: 0.8247 (p0) cc_final: 0.7998 (p0) REVERT: F 361 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7823 (ptp) REVERT: F 442 LYS cc_start: 0.7437 (mtmt) cc_final: 0.7104 (mtmm) REVERT: F 445 GLN cc_start: 0.7676 (mp10) cc_final: 0.7437 (mp10) REVERT: F 451 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8392 (t) REVERT: F 480 ASN cc_start: 0.4142 (OUTLIER) cc_final: 0.3739 (t0) REVERT: F 806 GLN cc_start: 0.6245 (OUTLIER) cc_final: 0.5491 (mm-40) REVERT: F 844 CYS cc_start: 0.4674 (OUTLIER) cc_final: 0.4120 (m) REVERT: F 1065 ASN cc_start: 0.6225 (t0) cc_final: 0.5955 (t0) outliers start: 93 outliers final: 44 residues processed: 323 average time/residue: 0.4982 time to fit residues: 189.5543 Evaluate side-chains 277 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 219 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 883 MET Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1352 CYS Chi-restraints excluded: chain A residue 1366 MET Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1387 LEU Chi-restraints excluded: chain A residue 1471 VAL Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 480 ASN Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 585 SER Chi-restraints excluded: chain F residue 687 ASN Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 797 VAL Chi-restraints excluded: chain F residue 806 GLN Chi-restraints excluded: chain F residue 844 CYS Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 0.0270 chunk 76 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 140 optimal weight: 0.0050 chunk 103 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 overall best weight: 0.5654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 294 GLN A 123 ASN A 418 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 663 ASN A 916 HIS A 948 GLN ** A 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN F 570 ASN F 697 ASN ** F 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 867 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.231325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.192676 restraints weight = 39231.073| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 4.60 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4092 r_free = 0.4092 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4092 r_free = 0.4092 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22320 Z= 0.120 Angle : 0.651 15.120 30312 Z= 0.319 Chirality : 0.045 0.467 3478 Planarity : 0.004 0.061 3794 Dihedral : 5.900 86.699 2942 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.33 % Allowed : 19.24 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -1.01 (0.16), residues: 2659 helix: 0.10 (0.14), residues: 1314 sheet: -0.49 (0.32), residues: 262 loop : -1.62 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 199 TYR 0.024 0.001 TYR F1071 PHE 0.022 0.001 PHE A1187 TRP 0.016 0.001 TRP E 212 HIS 0.005 0.001 HIS F 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (22283) covalent geometry : angle 0.62995 / 0.31 (30217) SS BOND : bond 0.00591 / 0.27 ( 13) SS BOND : angle 2.17363 / 1.08 ( 26) hydrogen bonds : bond 0.03698 / 2.44 ( 896) hydrogen bonds : angle 4.31556 / 2.95 ( 2579) Misc. bond : bond 0.00003 / 0.00 ( 1) link_BETA1-3 : bond 0.00988 / 0.49 ( 3) link_BETA1-3 : angle 1.19425 / 0.61 ( 9) link_BETA1-4 : bond 0.00810 / 0.34 ( 7) link_BETA1-4 : angle 2.11049 / 1.10 ( 21) link_NAG-ASN : bond 0.00865 / 0.44 ( 13) link_NAG-ASN : angle 3.98624 / 2.30 ( 39) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 240 time to evaluate : 0.779 Fit side-chains Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.5177 (mmm) cc_final: 0.4952 (tpp) REVERT: E 133 ARG cc_start: 0.5608 (OUTLIER) cc_final: 0.5169 (mpt-90) REVERT: A 51 LYS cc_start: 0.4552 (OUTLIER) cc_final: 0.3526 (tppp) REVERT: A 182 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6219 (tp) REVERT: A 194 LEU cc_start: 0.6040 (mm) cc_final: 0.5389 (mp) REVERT: A 343 LYS cc_start: 0.5066 (OUTLIER) cc_final: 0.4778 (mtmm) REVERT: A 519 MET cc_start: 0.1617 (mpp) cc_final: 0.1021 (mtt) REVERT: A 875 VAL cc_start: 0.5407 (OUTLIER) cc_final: 0.5090 (t) REVERT: A 965 GLU cc_start: 0.7353 (tt0) cc_final: 0.7086 (tt0) REVERT: A 1058 ASN cc_start: 0.6527 (m110) cc_final: 0.6151 (m-40) REVERT: A 1070 GLU cc_start: 0.4721 (tt0) cc_final: 0.4271 (tm-30) REVERT: A 1288 MET cc_start: 0.7153 (mmp) cc_final: 0.6609 (mpt) REVERT: A 1318 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7130 (ttt180) REVERT: A 1350 TYR cc_start: 0.7146 (m-10) cc_final: 0.6708 (m-10) REVERT: A 1373 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7963 (mt) REVERT: A 1475 LEU cc_start: 0.1675 (OUTLIER) cc_final: 0.1390 (mp) REVERT: F 202 ASP cc_start: 0.6066 (t0) cc_final: 0.5321 (m-30) REVERT: F 227 ASP cc_start: 0.5434 (m-30) cc_final: 0.5133 (t70) REVERT: F 256 MET cc_start: 0.8202 (ttm) cc_final: 0.7961 (ttp) REVERT: F 271 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8552 (tm) REVERT: F 302 ASP cc_start: 0.7024 (p0) cc_final: 0.6712 (p0) REVERT: F 361 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7037 (ptp) REVERT: F 442 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7082 (mtmm) REVERT: F 451 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8411 (t) REVERT: F 480 ASN cc_start: 0.4558 (OUTLIER) cc_final: 0.4226 (t0) REVERT: F 806 GLN cc_start: 0.5943 (OUTLIER) cc_final: 0.5542 (mm-40) REVERT: F 844 CYS cc_start: 0.3995 (OUTLIER) cc_final: 0.3605 (m) REVERT: F 1065 ASN cc_start: 0.5256 (t0) cc_final: 0.5013 (t0) outliers start: 100 outliers final: 41 residues processed: 311 average time/residue: 0.5050 time to fit residues: 185.0903 Evaluate side-chains 287 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 231 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1366 MET Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1471 VAL Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 442 LYS Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 480 ASN Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 687 ASN Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 797 VAL Chi-restraints excluded: chain F residue 806 GLN Chi-restraints excluded: chain F residue 844 CYS Chi-restraints excluded: chain F residue 849 ASP Chi-restraints excluded: chain F residue 886 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 138 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 209 GLN A 123 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 916 HIS ** A 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 ASN ** F 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 867 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.230074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.186102 restraints weight = 29744.093| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 5.61 r_work: 0.3473 rms_B_bonded: 5.08 restraints_weight: 2.0000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 22320 Z= 0.134 Angle : 0.677 16.095 30312 Z= 0.331 Chirality : 0.046 0.476 3478 Planarity : 0.005 0.060 3794 Dihedral : 5.862 87.871 2941 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 4.51 % Allowed : 19.71 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.83 (0.16), residues: 2659 helix: 0.27 (0.14), residues: 1312 sheet: -0.48 (0.32), residues: 252 loop : -1.54 (0.18), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 199 TYR 0.026 0.001 TYR F1071 PHE 0.027 0.002 PHE A 131 TRP 0.015 0.001 TRP A1112 HIS 0.005 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (22283) covalent geometry : angle 0.65428 / 0.33 (30217) SS BOND : bond 0.00362 / 0.20 ( 13) SS BOND : angle 2.46208 / 1.37 ( 26) hydrogen bonds : bond 0.03836 / 2.52 ( 896) hydrogen bonds : angle 4.30287 / 2.94 ( 2579) Misc. bond : bond 0.00003 / 0.00 ( 1) link_BETA1-3 : bond 0.00973 / 0.48 ( 3) link_BETA1-3 : angle 1.07580 / 0.53 ( 9) link_BETA1-4 : bond 0.00739 / 0.31 ( 7) link_BETA1-4 : angle 2.11887 / 1.11 ( 21) link_NAG-ASN : bond 0.01083 / 0.53 ( 13) link_NAG-ASN : angle 4.19542 / 2.50 ( 39) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 236 time to evaluate : 0.817 Fit side-chains Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 24 MET cc_start: 0.4378 (mmm) cc_final: 0.3996 (tpp) REVERT: E 120 MET cc_start: 0.5834 (mmm) cc_final: 0.5154 (tpp) REVERT: E 133 ARG cc_start: 0.5510 (OUTLIER) cc_final: 0.4840 (mpt-90) REVERT: A 182 LEU cc_start: 0.6806 (OUTLIER) cc_final: 0.6430 (tp) REVERT: A 194 LEU cc_start: 0.6422 (mm) cc_final: 0.5844 (mp) REVERT: A 519 MET cc_start: 0.1202 (mpp) cc_final: 0.0595 (mtt) REVERT: A 789 ARG cc_start: 0.1718 (mmt-90) cc_final: 0.1394 (ttt180) REVERT: A 875 VAL cc_start: 0.5201 (OUTLIER) cc_final: 0.4814 (t) REVERT: A 908 ILE cc_start: 0.5810 (OUTLIER) cc_final: 0.5264 (pp) REVERT: A 914 LEU cc_start: 0.6046 (OUTLIER) cc_final: 0.5306 (tt) REVERT: A 965 GLU cc_start: 0.8310 (tt0) cc_final: 0.8084 (tt0) REVERT: A 1058 ASN cc_start: 0.7321 (m110) cc_final: 0.7050 (m-40) REVERT: A 1070 GLU cc_start: 0.5082 (tt0) cc_final: 0.4307 (tm-30) REVERT: A 1125 PHE cc_start: 0.7225 (m-80) cc_final: 0.5966 (t80) REVERT: A 1242 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6749 (ptp-170) REVERT: A 1288 MET cc_start: 0.8099 (mmp) cc_final: 0.7614 (mmm) REVERT: A 1318 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7438 (ttt180) REVERT: A 1350 TYR cc_start: 0.7790 (m-10) cc_final: 0.7279 (m-10) REVERT: A 1373 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8181 (mt) REVERT: A 1475 LEU cc_start: 0.2543 (OUTLIER) cc_final: 0.2234 (mp) REVERT: F 58 VAL cc_start: 0.7835 (t) cc_final: 0.7476 (m) REVERT: F 202 ASP cc_start: 0.6289 (t0) cc_final: 0.5229 (m-30) REVERT: F 227 ASP cc_start: 0.6062 (m-30) cc_final: 0.5310 (t70) REVERT: F 270 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8010 (m) REVERT: F 302 ASP cc_start: 0.8294 (p0) cc_final: 0.8047 (p0) REVERT: F 361 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8048 (ptp) REVERT: F 430 ASP cc_start: 0.7759 (m-30) cc_final: 0.7533 (m-30) REVERT: F 451 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8487 (t) REVERT: F 480 ASN cc_start: 0.4008 (OUTLIER) cc_final: 0.3638 (t0) REVERT: F 669 TYR cc_start: 0.7304 (m-80) cc_final: 0.7075 (m-80) REVERT: F 806 GLN cc_start: 0.6196 (OUTLIER) cc_final: 0.5482 (mm110) REVERT: F 1020 MET cc_start: 0.6633 (ttt) cc_final: 0.6399 (ptm) REVERT: F 1065 ASN cc_start: 0.6120 (t0) cc_final: 0.5838 (t0) outliers start: 104 outliers final: 54 residues processed: 313 average time/residue: 0.5023 time to fit residues: 186.0582 Evaluate side-chains 298 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 230 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1242 ARG Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1373 ILE Chi-restraints excluded: chain A residue 1471 VAL Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 474 GLN Chi-restraints excluded: chain F residue 480 ASN Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 589 THR Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 687 ASN Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 704 LEU Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 797 VAL Chi-restraints excluded: chain F residue 806 GLN Chi-restraints excluded: chain F residue 825 ILE Chi-restraints excluded: chain F residue 849 ASP Chi-restraints excluded: chain F residue 1019 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 254 optimal weight: 0.1980 chunk 242 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 203 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 17 optimal weight: 6.9990 chunk 207 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 201 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 497 ASN A 916 HIS ** A 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 867 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.229434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.189206 restraints weight = 33785.360| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 4.70 r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4048 r_free = 0.4048 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22320 Z= 0.130 Angle : 0.667 14.275 30312 Z= 0.325 Chirality : 0.046 0.476 3478 Planarity : 0.004 0.060 3794 Dihedral : 5.734 89.439 2941 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 4.33 % Allowed : 20.15 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.68 (0.16), residues: 2659 helix: 0.39 (0.14), residues: 1314 sheet: -0.28 (0.30), residues: 277 loop : -1.51 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 199 TYR 0.030 0.001 TYR F1071 PHE 0.019 0.001 PHE A1187 TRP 0.016 0.001 TRP A1112 HIS 0.005 0.001 HIS A 992 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (22283) covalent geometry : angle 0.64616 / 0.32 (30217) SS BOND : bond 0.00396 / 0.21 ( 13) SS BOND : angle 2.38354 / 1.32 ( 26) hydrogen bonds : bond 0.03755 / 2.47 ( 896) hydrogen bonds : angle 4.27288 / 2.92 ( 2579) Misc. bond : bond 0.00009 / 0.00 ( 1) link_BETA1-3 : bond 0.00965 / 0.48 ( 3) link_BETA1-3 : angle 1.19339 / 0.59 ( 9) link_BETA1-4 : bond 0.00780 / 0.32 ( 7) link_BETA1-4 : angle 2.12347 / 1.11 ( 21) link_NAG-ASN : bond 0.00897 / 0.45 ( 13) link_NAG-ASN : angle 3.93159 / 2.32 ( 39) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 248 time to evaluate : 0.798 Fit side-chains Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 24 MET cc_start: 0.3608 (mmm) cc_final: 0.3368 (tpp) REVERT: E 215 CYS cc_start: 0.5326 (OUTLIER) cc_final: 0.4306 (m) REVERT: C 301 LEU cc_start: 0.0891 (pp) cc_final: 0.0664 (pp) REVERT: A 182 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6406 (tp) REVERT: A 194 LEU cc_start: 0.5998 (mm) cc_final: 0.5431 (mp) REVERT: A 519 MET cc_start: 0.1855 (OUTLIER) cc_final: 0.1182 (mtt) REVERT: A 789 ARG cc_start: 0.2379 (mmt-90) cc_final: 0.2050 (ttt180) REVERT: A 875 VAL cc_start: 0.5856 (OUTLIER) cc_final: 0.5403 (t) REVERT: A 908 ILE cc_start: 0.5705 (OUTLIER) cc_final: 0.5216 (pp) REVERT: A 914 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.5402 (tt) REVERT: A 1058 ASN cc_start: 0.6602 (m110) cc_final: 0.6271 (m-40) REVERT: A 1070 GLU cc_start: 0.4793 (tt0) cc_final: 0.4325 (tm-30) REVERT: A 1125 PHE cc_start: 0.7088 (m-80) cc_final: 0.6351 (t80) REVERT: A 1288 MET cc_start: 0.7151 (mmp) cc_final: 0.6574 (mmm) REVERT: A 1318 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7232 (ttt180) REVERT: A 1350 TYR cc_start: 0.6963 (m-10) cc_final: 0.6425 (m-10) REVERT: A 1475 LEU cc_start: 0.2014 (OUTLIER) cc_final: 0.1559 (mp) REVERT: F 58 VAL cc_start: 0.7182 (t) cc_final: 0.6960 (m) REVERT: F 202 ASP cc_start: 0.6066 (t0) cc_final: 0.5330 (m-30) REVERT: F 227 ASP cc_start: 0.5320 (m-30) cc_final: 0.5012 (t70) REVERT: F 302 ASP cc_start: 0.7128 (p0) cc_final: 0.6742 (p0) REVERT: F 361 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7076 (ptp) REVERT: F 414 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7605 (mt-10) REVERT: F 430 ASP cc_start: 0.7228 (m-30) cc_final: 0.6874 (m-30) REVERT: F 451 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8453 (t) REVERT: F 480 ASN cc_start: 0.4562 (OUTLIER) cc_final: 0.4192 (t0) REVERT: F 806 GLN cc_start: 0.5856 (OUTLIER) cc_final: 0.5463 (mm-40) REVERT: F 1065 ASN cc_start: 0.5391 (t0) cc_final: 0.5159 (t0) outliers start: 100 outliers final: 53 residues processed: 319 average time/residue: 0.4926 time to fit residues: 185.2235 Evaluate side-chains 298 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 233 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1393 ILE Chi-restraints excluded: chain A residue 1471 VAL Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 480 ASN Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 585 SER Chi-restraints excluded: chain F residue 589 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 687 ASN Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 797 VAL Chi-restraints excluded: chain F residue 806 GLN Chi-restraints excluded: chain F residue 849 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 29 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 169 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 209 GLN A 123 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 456 GLN ** A 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1131 ASN F 297 ASN ** F 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 867 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.228511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.184269 restraints weight = 29482.195| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 5.48 r_work: 0.3465 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22320 Z= 0.137 Angle : 0.680 13.861 30312 Z= 0.331 Chirality : 0.046 0.474 3478 Planarity : 0.005 0.059 3794 Dihedral : 5.570 88.932 2938 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.30 % Rotamer: Outliers : 3.86 % Allowed : 20.80 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.65 (0.16), residues: 2659 helix: 0.45 (0.14), residues: 1307 sheet: -0.20 (0.30), residues: 285 loop : -1.58 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 199 TYR 0.030 0.002 TYR F1071 PHE 0.031 0.002 PHE A 131 TRP 0.018 0.002 TRP A1112 HIS 0.010 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (22283) covalent geometry : angle 0.66096 / 0.33 (30217) SS BOND : bond 0.00385 / 0.19 ( 13) SS BOND : angle 2.19437 / 1.21 ( 26) hydrogen bonds : bond 0.03893 / 2.57 ( 896) hydrogen bonds : angle 4.30061 / 2.94 ( 2579) Misc. bond : bond 0.00063 / 0.03 ( 1) link_BETA1-3 : bond 0.01000 / 0.50 ( 3) link_BETA1-3 : angle 1.14440 / 0.55 ( 9) link_BETA1-4 : bond 0.00849 / 0.35 ( 7) link_BETA1-4 : angle 2.17995 / 1.13 ( 21) link_NAG-ASN : bond 0.00892 / 0.44 ( 13) link_NAG-ASN : angle 3.81557 / 2.26 ( 39) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 243 time to evaluate : 0.826 Fit side-chains Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 ARG cc_start: 0.4195 (ttm-80) cc_final: 0.3723 (mtp180) REVERT: E 24 MET cc_start: 0.4001 (mmm) cc_final: 0.3634 (tpp) REVERT: E 120 MET cc_start: 0.6383 (tpp) cc_final: 0.4457 (mmt) REVERT: E 215 CYS cc_start: 0.5828 (OUTLIER) cc_final: 0.4580 (m) REVERT: A 182 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6384 (tp) REVERT: A 194 LEU cc_start: 0.6548 (mm) cc_final: 0.6018 (mp) REVERT: A 449 ILE cc_start: 0.6842 (mm) cc_final: 0.6639 (mm) REVERT: A 519 MET cc_start: 0.1482 (mpp) cc_final: 0.0784 (mtt) REVERT: A 657 LEU cc_start: 0.5841 (OUTLIER) cc_final: 0.5533 (tt) REVERT: A 789 ARG cc_start: 0.1707 (mmt-90) cc_final: 0.1373 (ttt180) REVERT: A 875 VAL cc_start: 0.5556 (OUTLIER) cc_final: 0.5156 (t) REVERT: A 908 ILE cc_start: 0.5599 (OUTLIER) cc_final: 0.5148 (pp) REVERT: A 914 LEU cc_start: 0.6032 (OUTLIER) cc_final: 0.5385 (tt) REVERT: A 1070 GLU cc_start: 0.5172 (tt0) cc_final: 0.4388 (tm-30) REVERT: A 1125 PHE cc_start: 0.7249 (m-80) cc_final: 0.6001 (t80) REVERT: A 1288 MET cc_start: 0.8095 (mmp) cc_final: 0.7816 (mmm) REVERT: A 1318 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7462 (ttt180) REVERT: A 1350 TYR cc_start: 0.7635 (m-10) cc_final: 0.7221 (m-10) REVERT: A 1475 LEU cc_start: 0.1869 (OUTLIER) cc_final: 0.1547 (mp) REVERT: F 58 VAL cc_start: 0.7715 (t) cc_final: 0.7218 (m) REVERT: F 227 ASP cc_start: 0.6082 (m-30) cc_final: 0.5379 (t70) REVERT: F 302 ASP cc_start: 0.8247 (p0) cc_final: 0.7963 (p0) REVERT: F 414 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8483 (mt-10) REVERT: F 451 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8538 (t) REVERT: F 480 ASN cc_start: 0.3990 (OUTLIER) cc_final: 0.3603 (t0) REVERT: F 806 GLN cc_start: 0.6060 (OUTLIER) cc_final: 0.5480 (mm-40) REVERT: F 844 CYS cc_start: 0.4888 (OUTLIER) cc_final: 0.4291 (m) REVERT: F 1065 ASN cc_start: 0.6220 (t0) cc_final: 0.5919 (t0) outliers start: 89 outliers final: 59 residues processed: 307 average time/residue: 0.4841 time to fit residues: 175.5653 Evaluate side-chains 302 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 231 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1129 MET Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1471 VAL Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 480 ASN Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 585 SER Chi-restraints excluded: chain F residue 589 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 687 ASN Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 797 VAL Chi-restraints excluded: chain F residue 806 GLN Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 844 CYS Chi-restraints excluded: chain F residue 849 ASP Chi-restraints excluded: chain F residue 900 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 238 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 209 GLN A 123 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 ASN A1287 GLN F 120 ASN F 297 ASN ** F 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 687 ASN ** F 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 867 HIS ** F1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.227513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.187588 restraints weight = 35210.751| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 4.72 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4028 r_free = 0.4028 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.4028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.5029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 22320 Z= 0.189 Angle : 0.808 59.113 30312 Z= 0.430 Chirality : 0.049 0.791 3478 Planarity : 0.005 0.059 3794 Dihedral : 5.578 89.007 2936 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.78 % Favored : 95.11 % Rotamer: Outliers : 3.86 % Allowed : 21.06 % Favored : 75.09 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2659 helix: 0.44 (0.14), residues: 1308 sheet: -0.21 (0.30), residues: 285 loop : -1.58 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 584 TYR 0.027 0.002 TYR F1071 PHE 0.017 0.002 PHE A1187 TRP 0.016 0.002 TRP A1112 HIS 0.008 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (22283) covalent geometry : angle 0.79265 / 0.43 (30217) SS BOND : bond 0.00387 / 0.19 ( 13) SS BOND : angle 2.08557 / 1.16 ( 26) hydrogen bonds : bond 0.03984 / 2.62 ( 896) hydrogen bonds : angle 4.30426 / 2.94 ( 2579) Misc. bond : bond 0.00043 / 0.02 ( 1) link_BETA1-3 : bond 0.00984 / 0.49 ( 3) link_BETA1-3 : angle 1.14479 / 0.54 ( 9) link_BETA1-4 : bond 0.00442 / 0.20 ( 7) link_BETA1-4 : angle 2.31516 / 1.20 ( 21) link_NAG-ASN : bond 0.00901 / 0.44 ( 13) link_NAG-ASN : angle 3.81336 / 2.26 ( 39) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 230 time to evaluate : 0.779 Fit side-chains Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 ARG cc_start: 0.4214 (ttm-80) cc_final: 0.3749 (mtp180) REVERT: E 24 MET cc_start: 0.3581 (mmm) cc_final: 0.3380 (tpp) REVERT: E 215 CYS cc_start: 0.5681 (OUTLIER) cc_final: 0.4631 (m) REVERT: A 182 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6401 (tp) REVERT: A 194 LEU cc_start: 0.6106 (mm) cc_final: 0.5560 (mp) REVERT: A 449 ILE cc_start: 0.6283 (mm) cc_final: 0.5990 (mm) REVERT: A 519 MET cc_start: 0.1889 (OUTLIER) cc_final: 0.1191 (mtt) REVERT: A 789 ARG cc_start: 0.2177 (mmt-90) cc_final: 0.1880 (ttt180) REVERT: A 875 VAL cc_start: 0.5963 (OUTLIER) cc_final: 0.5448 (t) REVERT: A 908 ILE cc_start: 0.5628 (OUTLIER) cc_final: 0.5147 (pp) REVERT: A 914 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5449 (tt) REVERT: A 1070 GLU cc_start: 0.4770 (tt0) cc_final: 0.4286 (tm-30) REVERT: A 1125 PHE cc_start: 0.7092 (m-80) cc_final: 0.6369 (t80) REVERT: A 1288 MET cc_start: 0.7209 (mmp) cc_final: 0.6669 (mmm) REVERT: A 1318 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7361 (ttt180) REVERT: A 1350 TYR cc_start: 0.6881 (m-10) cc_final: 0.6475 (m-10) REVERT: A 1475 LEU cc_start: 0.1316 (OUTLIER) cc_final: 0.1032 (mp) REVERT: F 58 VAL cc_start: 0.7264 (t) cc_final: 0.6947 (m) REVERT: F 227 ASP cc_start: 0.5518 (m-30) cc_final: 0.5152 (t70) REVERT: F 302 ASP cc_start: 0.7138 (p0) cc_final: 0.6708 (p0) REVERT: F 336 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7602 (mmtp) REVERT: F 414 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7643 (mt-10) REVERT: F 451 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8511 (t) REVERT: F 480 ASN cc_start: 0.4613 (OUTLIER) cc_final: 0.4270 (t0) REVERT: F 806 GLN cc_start: 0.5849 (OUTLIER) cc_final: 0.5636 (mm-40) REVERT: F 844 CYS cc_start: 0.4200 (OUTLIER) cc_final: 0.3702 (m) REVERT: F 1065 ASN cc_start: 0.5420 (t0) cc_final: 0.5155 (t0) outliers start: 89 outliers final: 65 residues processed: 292 average time/residue: 0.4854 time to fit residues: 167.6019 Evaluate side-chains 306 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 228 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1129 MET Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1393 ILE Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1471 VAL Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 480 ASN Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 585 SER Chi-restraints excluded: chain F residue 589 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 797 VAL Chi-restraints excluded: chain F residue 806 GLN Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 844 CYS Chi-restraints excluded: chain F residue 849 ASP Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 187 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 226 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 168 optimal weight: 0.0170 chunk 100 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 250 optimal weight: 0.7980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 209 GLN A 123 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 ASN A1287 GLN F 120 ASN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 867 HIS ** F1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.227541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.191858 restraints weight = 31522.493| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 3.84 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4096 r_free = 0.4096 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4096 r_free = 0.4096 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.4096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.270 22320 Z= 0.210 Angle : 0.817 59.113 30312 Z= 0.434 Chirality : 0.049 0.791 3478 Planarity : 0.005 0.059 3794 Dihedral : 5.578 89.007 2936 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.78 % Favored : 95.11 % Rotamer: Outliers : 3.47 % Allowed : 21.58 % Favored : 74.96 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2659 helix: 0.44 (0.14), residues: 1308 sheet: -0.21 (0.30), residues: 285 loop : -1.58 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 584 TYR 0.027 0.002 TYR F1071 PHE 0.017 0.002 PHE A1187 TRP 0.016 0.002 TRP A1112 HIS 0.008 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (22283) covalent geometry : angle 0.79265 / 0.43 (30217) SS BOND : bond 0.07494 / 3.75 ( 13) SS BOND : angle 4.54377 / 2.06 ( 26) hydrogen bonds : bond 0.03984 / 2.62 ( 896) hydrogen bonds : angle 4.30426 / 2.94 ( 2579) Misc. bond : bond 0.00043 / 0.02 ( 1) link_BETA1-3 : bond 0.00984 / 0.49 ( 3) link_BETA1-3 : angle 1.14478 / 0.54 ( 9) link_BETA1-4 : bond 0.00442 / 0.20 ( 7) link_BETA1-4 : angle 2.31517 / 1.20 ( 21) link_NAG-ASN : bond 0.00901 / 0.44 ( 13) link_NAG-ASN : angle 3.81336 / 2.26 ( 39) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5318 Ramachandran restraints generated. 2659 Oldfield, 0 Emsley, 2659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 229 time to evaluate : 0.812 Fit side-chains Corrupt residue: chain: B residue: PRO 115 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 ARG cc_start: 0.4149 (ttm-80) cc_final: 0.3667 (mtp180) REVERT: E 215 CYS cc_start: 0.5654 (OUTLIER) cc_final: 0.4618 (m) REVERT: A 182 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6362 (tp) REVERT: A 194 LEU cc_start: 0.6144 (mm) cc_final: 0.5593 (mp) REVERT: A 449 ILE cc_start: 0.6275 (mm) cc_final: 0.5991 (mm) REVERT: A 519 MET cc_start: 0.1940 (OUTLIER) cc_final: 0.1232 (mtt) REVERT: A 789 ARG cc_start: 0.2322 (mmt-90) cc_final: 0.2052 (ttt180) REVERT: A 875 VAL cc_start: 0.5976 (OUTLIER) cc_final: 0.5457 (t) REVERT: A 908 ILE cc_start: 0.5576 (OUTLIER) cc_final: 0.5114 (pp) REVERT: A 914 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5462 (tt) REVERT: A 1070 GLU cc_start: 0.4750 (tt0) cc_final: 0.4364 (tm-30) REVERT: A 1125 PHE cc_start: 0.7080 (m-80) cc_final: 0.6421 (t80) REVERT: A 1288 MET cc_start: 0.7236 (mmp) cc_final: 0.6683 (mmm) REVERT: A 1318 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7358 (ttt180) REVERT: A 1350 TYR cc_start: 0.6759 (m-10) cc_final: 0.6359 (m-10) REVERT: A 1475 LEU cc_start: 0.1125 (OUTLIER) cc_final: 0.0855 (mp) REVERT: F 58 VAL cc_start: 0.7239 (t) cc_final: 0.6941 (m) REVERT: F 227 ASP cc_start: 0.5501 (m-30) cc_final: 0.5137 (t70) REVERT: F 302 ASP cc_start: 0.7136 (p0) cc_final: 0.6701 (p0) REVERT: F 336 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7607 (mmtp) REVERT: F 414 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7643 (mt-10) REVERT: F 451 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8504 (t) REVERT: F 480 ASN cc_start: 0.4622 (OUTLIER) cc_final: 0.4287 (t0) REVERT: F 844 CYS cc_start: 0.4102 (OUTLIER) cc_final: 0.3635 (m) REVERT: F 1065 ASN cc_start: 0.5390 (t0) cc_final: 0.5126 (t0) outliers start: 80 outliers final: 65 residues processed: 285 average time/residue: 0.4950 time to fit residues: 166.8190 Evaluate side-chains 305 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 228 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain B residue 115 PRO Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 361 GLU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 543 THR Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 588 GLU Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain A residue 908 ILE Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 921 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 981 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1098 LEU Chi-restraints excluded: chain A residue 1129 MET Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1318 ARG Chi-restraints excluded: chain A residue 1333 SER Chi-restraints excluded: chain A residue 1351 THR Chi-restraints excluded: chain A residue 1393 ILE Chi-restraints excluded: chain A residue 1420 LEU Chi-restraints excluded: chain A residue 1471 VAL Chi-restraints excluded: chain A residue 1475 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 281 MET Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 336 LYS Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 407 GLU Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 480 ASN Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 579 LYS Chi-restraints excluded: chain F residue 585 SER Chi-restraints excluded: chain F residue 589 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 710 LEU Chi-restraints excluded: chain F residue 743 ILE Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 797 VAL Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 844 CYS Chi-restraints excluded: chain F residue 849 ASP Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 900 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 69 optimal weight: 0.0770 chunk 120 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 0.1980 chunk 87 optimal weight: 4.9990 chunk 228 optimal weight: 0.7980 chunk 218 optimal weight: 0.4980 chunk 180 optimal weight: 0.1980 chunk 128 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 198 optimal weight: 0.3980 overall best weight: 0.2738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 209 GLN A 123 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 ASN A1287 GLN F 120 ASN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 867 HIS ** F1039 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.228152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.185140 restraints weight = 37417.169| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 5.26 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.175 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.270 22320 Z= 0.210 Angle : 0.817 59.113 30312 Z= 0.434 Chirality : 0.049 0.791 3478 Planarity : 0.005 0.059 3794 Dihedral : 5.578 89.007 2936 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.78 % Favored : 95.11 % Rotamer: Outliers : 3.42 % Allowed : 21.66 % Favored : 74.91 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.16), residues: 2659 helix: 0.44 (0.14), residues: 1308 sheet: -0.21 (0.30), residues: 285 loop : -1.58 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 584 TYR 0.027 0.002 TYR F1071 PHE 0.017 0.002 PHE A1187 TRP 0.016 0.002 TRP A1112 HIS 0.008 0.001 HIS A 916 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (22283) covalent geometry : angle 0.79265 / 0.43 (30217) SS BOND : bond 0.07494 / 3.75 ( 13) SS BOND : angle 4.54371 / 2.06 ( 26) hydrogen bonds : bond 0.03984 / 2.62 ( 896) hydrogen bonds : angle 4.30426 / 2.94 ( 2579) Misc. bond : bond 0.00043 / 0.02 ( 1) link_BETA1-3 : bond 0.00984 / 0.49 ( 3) link_BETA1-3 : angle 1.14478 / 0.54 ( 9) link_BETA1-4 : bond 0.00442 / 0.20 ( 7) link_BETA1-4 : angle 2.31517 / 1.20 ( 21) link_NAG-ASN : bond 0.00901 / 0.44 ( 13) link_NAG-ASN : angle 3.81336 / 2.26 ( 39) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8223.97 seconds wall clock time: 140 minutes 50.47 seconds (8450.47 seconds total)