Starting phenix.real_space_refine on Sat Jul 4 14:07:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uum_64512/07_2026/9uum_64512.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uum_64512/07_2026/9uum_64512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uum_64512/07_2026/9uum_64512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uum_64512/07_2026/9uum_64512.map" model { file = "/net/cci-nas-00/data/ceres_data/9uum_64512/07_2026/9uum_64512.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uum_64512/07_2026/9uum_64512.cif" } resolution = 3.41 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= 0.034 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 Zn 6 6.06 5 S 125 5.16 5 C 13228 2.51 5 N 3571 2.21 5 O 3876 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20807 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 2945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2945 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 20, 'TRANS': 360} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 9, 'HIS:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "D" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1142 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 15, 'TRANS': 130} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 596 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "U" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 583 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 660 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 8682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8682 Classifications: {'peptide': 1108} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 1067} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 5717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5717 Classifications: {'peptide': 699} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 679} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {' ZN': 1, 'QFC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2173 SG CYS C 323 97.921 42.752 101.451 1.00179.15 S ATOM 2189 SG CYS C 326 98.249 39.709 99.260 1.00172.74 S ATOM 2683 SG CYS C 391 98.921 39.492 103.062 1.00192.65 S ATOM 2702 SG CYS C 394 101.301 41.249 100.333 1.00196.34 S ATOM 4349 SG CYS I 176 126.575 56.183 99.647 1.00252.72 S ATOM 4373 SG CYS I 179 127.334 53.234 97.358 1.00260.22 S ATOM 4140 SG CYS I 148 111.058 46.860 109.834 1.00164.26 S ATOM 4163 SG CYS I 151 107.421 45.459 110.952 1.00194.82 S ATOM 5903 SG CYS R 42 138.296 53.341 78.660 1.00194.68 S ATOM 5922 SG CYS R 45 136.299 56.010 76.769 1.00192.30 S ATOM 6170 SG CYS R 83 137.533 56.769 80.346 1.00223.21 S ATOM 6099 SG CYS R 75 143.585 43.193 87.073 1.00221.02 S ATOM 6266 SG CYS R 94 140.620 45.692 85.938 1.00205.97 S ATOM 5989 SG CYS R 53 138.577 60.996 78.948 1.00244.13 S ATOM 6012 SG CYS R 56 140.282 64.033 77.313 1.00241.12 S ATOM 6049 SG CYS R 68 142.355 61.002 78.141 1.00234.91 S Time building chain proxies: 4.36, per 1000 atoms: 0.21 Number of scatterers: 20807 At special positions: 0 Unit cell: (186.75, 126.99, 141.1, 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) Zn 6 29.99 S 125 16.00 F 1 9.00 O 3876 8.00 N 3571 7.00 C 13228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 313 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 893.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 326 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 323 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 394 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 391 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" NE2 HIS I 196 " pdb="ZN ZN I 201 " - pdb=" NE2 HIS I 192 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 179 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 176 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" NE2 HIS I 164 " pdb="ZN ZN I 202 " - pdb=" NE2 HIS I 168 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 148 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 151 " pdb=" ZN R 201 " pdb="ZN ZN R 201 " - pdb=" ND1 HIS R 80 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 45 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 42 " pdb="ZN ZN R 201 " - pdb=" SG CYS R 83 " pdb=" ZN R 202 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 94 " pdb="ZN ZN R 202 " - pdb=" ND1 HIS R 77 " pdb="ZN ZN R 202 " - pdb=" SG CYS R 75 " pdb=" ZN R 203 " pdb="ZN ZN R 203 " - pdb=" ND1 HIS R 82 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 68 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 56 " pdb="ZN ZN R 203 " - pdb=" SG CYS R 53 " Number of angles added : 16 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 37 sheets defined 31.1% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.636A pdb=" N VAL C 107 " --> pdb=" O HIS C 103 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN C 115 " --> pdb=" O ARG C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 4.387A pdb=" N LYS C 204 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 removed outlier: 3.610A pdb=" N TRP C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 238 removed outlier: 4.085A pdb=" N ASN C 236 " --> pdb=" O HIS C 233 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 237 " --> pdb=" O CYS C 234 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 238 " --> pdb=" O ALA C 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 233 through 238' Processing helix chain 'C' and resid 241 through 247 removed outlier: 3.780A pdb=" N TYR C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 265 removed outlier: 3.599A pdb=" N GLN C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 286 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 303 through 317 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'D' and resid 3 through 16 removed outlier: 3.544A pdb=" N ASP D 16 " --> pdb=" O ASP D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.848A pdb=" N ARG D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 112 removed outlier: 3.743A pdb=" N CYS D 111 " --> pdb=" O CYS D 107 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 130 Processing helix chain 'D' and resid 131 through 145 Processing helix chain 'I' and resid 157 through 168 Processing helix chain 'I' and resid 186 through 197 removed outlier: 4.179A pdb=" N THR I 190 " --> pdb=" O ARG I 186 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY I 191 " --> pdb=" O ASP I 187 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER I 197 " --> pdb=" O LEU I 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 34 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'U' and resid 22 through 35 removed outlier: 4.330A pdb=" N VAL U 26 " --> pdb=" O THR U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 60 Processing helix chain 'R' and resid 80 through 91 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.609A pdb=" N ARG B 369 " --> pdb=" O ASP B 366 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN B 370 " --> pdb=" O LEU B 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 366 through 370' Processing helix chain 'B' and resid 987 through 990 removed outlier: 4.226A pdb=" N GLN B 990 " --> pdb=" O GLU B 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 987 through 990' Processing helix chain 'B' and resid 1044 through 1062 Processing helix chain 'B' and resid 1069 through 1074 Processing helix chain 'B' and resid 1091 through 1096 Processing helix chain 'B' and resid 1097 through 1100 removed outlier: 3.789A pdb=" N ILE B1100 " --> pdb=" O PHE B1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1097 through 1100' Processing helix chain 'B' and resid 1101 through 1109 Processing helix chain 'B' and resid 1125 through 1138 removed outlier: 3.673A pdb=" N LEU B1129 " --> pdb=" O THR B1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 75 Processing helix chain 'A' and resid 82 through 95 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.558A pdb=" N LEU A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 123 removed outlier: 4.121A pdb=" N GLU A 123 " --> pdb=" O PRO A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 153 removed outlier: 3.631A pdb=" N MET A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 169 through 182 Processing helix chain 'A' and resid 185 through 205 Processing helix chain 'A' and resid 210 through 224 removed outlier: 3.892A pdb=" N LEU A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET A 220 " --> pdb=" O SER A 216 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 245 removed outlier: 4.001A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA A 245 " --> pdb=" O CYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 252 removed outlier: 4.326A pdb=" N GLN A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 277 removed outlier: 3.618A pdb=" N TYR A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 282 through 295 removed outlier: 4.073A pdb=" N LEU A 286 " --> pdb=" O THR A 282 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 287 " --> pdb=" O GLN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 313 removed outlier: 4.973A pdb=" N ASP A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N HIS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.868A pdb=" N ARG A 328 " --> pdb=" O GLN A 324 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N VAL A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 354 removed outlier: 3.507A pdb=" N ALA A 335 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 359 removed outlier: 4.108A pdb=" N LYS A 359 " --> pdb=" O GLU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 379 Processing helix chain 'A' and resid 383 through 399 removed outlier: 4.282A pdb=" N ASN A 399 " --> pdb=" O GLU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 417 removed outlier: 3.774A pdb=" N GLU A 407 " --> pdb=" O ASN A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 441 Processing helix chain 'A' and resid 445 through 464 removed outlier: 3.834A pdb=" N PHE A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 484 Processing helix chain 'A' and resid 488 through 515 removed outlier: 3.545A pdb=" N GLU A 492 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N MET A 494 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N PHE A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS A 507 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN A 515 " --> pdb=" O HIS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 562 removed outlier: 3.731A pdb=" N PHE A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.839A pdb=" N MET A 615 " --> pdb=" O GLU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 634 Processing helix chain 'A' and resid 693 through 708 removed outlier: 3.587A pdb=" N ASP A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 723 removed outlier: 3.552A pdb=" N ASN A 721 " --> pdb=" O SER A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 742 Processing sheet with id=AA1, first strand: chain 'C' and resid 78 through 82 removed outlier: 3.776A pdb=" N ALA C 180 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 183 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 157 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 99 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 159 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 78 through 82 removed outlier: 3.776A pdb=" N ALA C 180 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN C 183 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS C 158 " --> pdb=" O TYR C 142 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR C 138 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ARG C 164 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY C 136 " --> pdb=" O ARG C 164 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 120 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AA4, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.847A pdb=" N THR C 418 " --> pdb=" O ILE C 398 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE C 398 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N HIS C 397 " --> pdb=" O CYS C 391 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N CYS C 391 " --> pdb=" O HIS C 397 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY C 399 " --> pdb=" O ALA C 389 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 21 through 25 removed outlier: 3.587A pdb=" N SER D 22 " --> pdb=" O THR D 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 146 through 147 removed outlier: 3.794A pdb=" N PHE I 146 " --> pdb=" O PHE I 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 12 through 13 removed outlier: 6.944A pdb=" N LYS N 4 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU N 69 " --> pdb=" O LYS N 4 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS N 6 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N LEU N 71 " --> pdb=" O LYS N 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'U' and resid 12 through 16 removed outlier: 3.835A pdb=" N SER U 65 " --> pdb=" O GLN U 2 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 522 through 523 removed outlier: 4.187A pdb=" N TRP R 27 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ASN A 526 " --> pdb=" O TRP R 27 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA R 29 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N LEU A 528 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA R 31 " --> pdb=" O LEU A 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 522 through 523 removed outlier: 4.187A pdb=" N TRP R 27 " --> pdb=" O ASP A 522 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS R 26 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N VAL R 30 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU A 573 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 12.531A pdb=" N LEU R 32 " --> pdb=" O THR A 571 " (cutoff:3.500A) removed outlier: 11.433A pdb=" N THR A 571 " --> pdb=" O LEU R 32 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'B' and resid 1007 through 1009 removed outlier: 6.705A pdb=" N ILE B1037 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B1089 " --> pdb=" O ASN B 4 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 6 " --> pdb=" O ILE B1089 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 15 through 21 removed outlier: 4.059A pdb=" N GLY B 17 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 34 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY B 21 " --> pdb=" O ASN B 30 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG B 38 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 53 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL B 43 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 63 through 67 removed outlier: 3.523A pdb=" N GLU B 65 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 67 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA B 86 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N HIS B 105 " --> pdb=" O ALA B 86 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE B 88 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 121 through 124 removed outlier: 3.793A pdb=" N ILE B 121 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS B 141 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 163 through 169 removed outlier: 4.569A pdb=" N HIS B 163 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP B 184 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 196 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU B 201 " --> pdb=" O SER B 196 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 163 through 169 removed outlier: 4.569A pdb=" N HIS B 163 " --> pdb=" O GLN B 183 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL B 181 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL B 167 " --> pdb=" O CYS B 179 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N CYS B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE B 169 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR B 177 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP B 184 " --> pdb=" O GLY B 187 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 218 through 221 Processing sheet with id=AC1, first strand: chain 'B' and resid 258 through 263 removed outlier: 3.824A pdb=" N CYS B 260 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP B 275 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU B 280 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LEU B 304 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N MET B 282 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL B 302 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU B 284 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU B 300 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLU B 286 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 313 through 318 removed outlier: 7.036A pdb=" N VAL B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N SER B 331 " --> pdb=" O THR B 352 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N THR B 352 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU B 333 " --> pdb=" O MET B 350 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 359 through 365 removed outlier: 4.193A pdb=" N ASP B 361 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 365 " --> pdb=" O GLN B 374 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 379 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 359 through 365 removed outlier: 4.193A pdb=" N ASP B 361 " --> pdb=" O CYS B 378 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 365 " --> pdb=" O GLN B 374 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER B 379 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 396 through 403 removed outlier: 5.656A pdb=" N GLU B 398 " --> pdb=" O THR B 703 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N THR B 703 " --> pdb=" O GLU B 398 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 400 " --> pdb=" O ILE B 701 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 411 through 413 removed outlier: 3.536A pdb=" N ARG B 434 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B 442 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 457 through 463 removed outlier: 6.640A pdb=" N ILE B 471 " --> pdb=" O PHE B 458 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS B 460 " --> pdb=" O ILE B 469 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE B 469 " --> pdb=" O CYS B 460 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN B 462 " --> pdb=" O GLN B 467 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLN B 467 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 488 " --> pdb=" O LEU B 478 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N SER B 480 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LEU B 486 " --> pdb=" O SER B 480 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 500 through 503 removed outlier: 3.643A pdb=" N VAL B 500 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 511 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 509 " --> pdb=" O SER B 502 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 510 " --> pdb=" O TYR B 517 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR B 532 " --> pdb=" O LEU B 516 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR B 518 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 530 " --> pdb=" O TYR B 518 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN B 520 " --> pdb=" O GLN B 528 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLN B 528 " --> pdb=" O GLN B 520 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N HIS B 522 " --> pdb=" O LEU B 526 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU B 526 " --> pdb=" O HIS B 522 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.341A pdb=" N GLY B 559 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 541 " --> pdb=" O ALA B 557 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA B 557 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS B 556 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 569 " --> pdb=" O CYS B 556 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N SER B 565 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS B 578 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 591 through 595 removed outlier: 3.514A pdb=" N THR B 594 " --> pdb=" O TYR B 601 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 611 " --> pdb=" O LYS B 628 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS B 628 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N TYR B 613 " --> pdb=" O ARG B 626 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ARG B 626 " --> pdb=" O TYR B 613 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER B 624 " --> pdb=" O GLY B 615 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 639 through 642 removed outlier: 9.109A pdb=" N THR B 647 " --> pdb=" O SER B 661 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER B 661 " --> pdb=" O THR B 647 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 720 through 727 removed outlier: 3.622A pdb=" N SER B 720 " --> pdb=" O SER B 738 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU B 736 " --> pdb=" O ARG B 722 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE B 724 " --> pdb=" O GLY B 734 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY B 734 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TYR B 726 " --> pdb=" O CYS B 732 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N CYS B 732 " --> pdb=" O TYR B 726 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER B 737 " --> pdb=" O ASN B 790 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N HIS B 789 " --> pdb=" O GLN B 806 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLN B 806 " --> pdb=" O HIS B 789 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU B 791 " --> pdb=" O ALA B 804 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA B 804 " --> pdb=" O LEU B 791 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 793 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 764 " --> pdb=" O ALA B 804 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 811 through 819 removed outlier: 6.083A pdb=" N ALA B 813 " --> pdb=" O ALA B 834 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ALA B 834 " --> pdb=" O ALA B 813 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS B 819 " --> pdb=" O TYR B 828 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B 847 " --> pdb=" O THR B 833 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 862 " --> pdb=" O VAL B 850 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLN B 852 " --> pdb=" O THR B 860 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N THR B 860 " --> pdb=" O GLN B 852 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N SER B 854 " --> pdb=" O LEU B 858 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU B 858 " --> pdb=" O SER B 854 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 874 through 875 Processing sheet with id=AD6, first strand: chain 'B' and resid 913 through 917 removed outlier: 3.519A pdb=" N TYR B 913 " --> pdb=" O GLY B 924 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 917 " --> pdb=" O PHE B 920 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 921 " --> pdb=" O LEU B 933 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 946 " --> pdb=" O LEU B 932 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA B 934 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLU B 944 " --> pdb=" O ALA B 934 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS B 936 " --> pdb=" O PHE B 942 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE B 942 " --> pdb=" O LYS B 936 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 957 through 961 removed outlier: 6.574A pdb=" N ASN B 964 " --> pdb=" O LEU B 960 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY B 996 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLN B 978 " --> pdb=" O GLU B 994 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU B 994 " --> pdb=" O GLN B 978 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1075 through 1078 Processing sheet with id=AD9, first strand: chain 'A' and resid 640 through 641 Processing sheet with id=AE1, first strand: chain 'A' and resid 746 through 747 removed outlier: 3.803A pdb=" N GLU A 746 " --> pdb=" O HIS A 756 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2298 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 3494 1.26 - 1.40: 5048 1.40 - 1.54: 12244 1.54 - 1.68: 243 1.68 - 1.81: 187 Bond restraints: 21216 Sorted by residual: bond pdb=" C7 QFC C 502 " pdb=" N1 QFC C 502 " ideal model delta sigma weight residual 1.458 1.283 0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" C29 QFC C 502 " pdb=" N1 QFC C 502 " ideal model delta sigma weight residual 1.458 1.296 0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" C2 QFC C 502 " pdb=" C31 QFC C 502 " ideal model delta sigma weight residual 1.420 1.533 -0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C8 QFC C 502 " pdb=" N1 QFC C 502 " ideal model delta sigma weight residual 1.463 1.350 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" N QFC C 502 " pdb=" C5 QFC C 502 " ideal model delta sigma weight residual 1.372 1.484 -0.112 2.00e-02 2.50e+03 3.13e+01 ... (remaining 21211 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 28122 1.68 - 3.36: 486 3.36 - 5.04: 66 5.04 - 6.72: 22 6.72 - 8.39: 3 Bond angle restraints: 28699 Sorted by residual: angle pdb=" C ARG A 742 " pdb=" N ASP A 743 " pdb=" CA ASP A 743 " ideal model delta sigma weight residual 121.54 128.01 -6.47 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C ARG B 928 " pdb=" N SER B 929 " pdb=" CA SER B 929 " ideal model delta sigma weight residual 121.54 127.76 -6.22 1.91e+00 2.74e-01 1.06e+01 angle pdb=" C PRO A 402 " pdb=" N ASN A 403 " pdb=" CA ASN A 403 " ideal model delta sigma weight residual 121.54 127.10 -5.56 1.91e+00 2.74e-01 8.48e+00 angle pdb=" N GLU B 224 " pdb=" CA GLU B 224 " pdb=" C GLU B 224 " ideal model delta sigma weight residual 109.81 116.10 -6.29 2.21e+00 2.05e-01 8.09e+00 angle pdb=" C ALA A 556 " pdb=" N PHE A 557 " pdb=" CA PHE A 557 " ideal model delta sigma weight residual 121.14 116.23 4.91 1.75e+00 3.27e-01 7.88e+00 ... (remaining 28694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.16: 11925 22.16 - 44.32: 815 44.32 - 66.48: 87 66.48 - 88.64: 41 88.64 - 110.80: 4 Dihedral angle restraints: 12872 sinusoidal: 5245 harmonic: 7627 Sorted by residual: dihedral pdb=" CB CYS B 18 " pdb=" SG CYS B 18 " pdb=" SG CYS B 313 " pdb=" CB CYS B 313 " ideal model delta sinusoidal sigma weight residual 93.00 147.94 -54.94 1 1.00e+01 1.00e-02 4.09e+01 dihedral pdb=" CA GLY A 306 " pdb=" C GLY A 306 " pdb=" N LEU A 307 " pdb=" CA LEU A 307 " ideal model delta harmonic sigma weight residual -180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PHE A 397 " pdb=" C PHE A 397 " pdb=" N ILE A 398 " pdb=" CA ILE A 398 " ideal model delta harmonic sigma weight residual -180.00 -158.43 -21.57 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 12869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2927 0.073 - 0.145: 308 0.145 - 0.218: 2 0.218 - 0.290: 0 0.290 - 0.363: 1 Chirality restraints: 3238 Sorted by residual: chirality pdb=" C22 QFC C 502 " pdb=" C23 QFC C 502 " pdb=" C26 QFC C 502 " pdb=" N2 QFC C 502 " both_signs ideal model delta sigma weight residual False -2.30 -2.66 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA ASP A 743 " pdb=" N ASP A 743 " pdb=" C ASP A 743 " pdb=" CB ASP A 743 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA THR C 332 " pdb=" N THR C 332 " pdb=" C THR C 332 " pdb=" CB THR C 332 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 3235 not shown) Planarity restraints: 3679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 950 " -0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO B 951 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 951 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 951 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B1122 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C ARG B1122 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG B1122 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU B1123 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1073 " -0.011 2.00e-02 2.50e+03 1.16e-02 3.37e+00 pdb=" CG TRP B1073 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP B1073 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B1073 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B1073 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B1073 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1073 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1073 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1073 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B1073 " 0.001 2.00e-02 2.50e+03 ... (remaining 3676 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 392 2.68 - 3.24: 19826 3.24 - 3.79: 29668 3.79 - 4.35: 38706 4.35 - 4.90: 65246 Nonbonded interactions: 153838 Sorted by model distance: nonbonded pdb=" OG1 THR U 9 " pdb=" OD1 ASN R 41 " model vdw 2.127 3.040 nonbonded pdb=" O GLN A 248 " pdb=" NE2 GLN A 252 " model vdw 2.168 3.120 nonbonded pdb=" OE2 GLU A 176 " pdb=" OG1 THR A 180 " model vdw 2.180 3.040 nonbonded pdb=" CE2 PHE C 150 " pdb=" F QFC C 502 " model vdw 2.182 3.290 nonbonded pdb=" OG1 THR B 102 " pdb=" O VAL B1065 " model vdw 2.195 3.040 ... (remaining 153833 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.540 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.175 21240 Z= 0.171 Angle : 0.576 9.283 28717 Z= 0.293 Chirality : 0.042 0.363 3238 Planarity : 0.004 0.057 3679 Dihedral : 14.968 110.800 7925 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.13 % Allowed : 0.18 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.16), residues: 2590 helix: 1.45 (0.20), residues: 715 sheet: -1.14 (0.23), residues: 565 loop : -1.80 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 369 TYR 0.015 0.001 TYR A 58 PHE 0.019 0.001 PHE A 557 TRP 0.031 0.002 TRP B1073 HIS 0.009 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (21216) covalent geometry : angle 0.56785 / 0.29 (28699) SS BOND : bond 0.00194 / 0.10 ( 1) SS BOND : angle 1.08868 / 0.61 ( 2) hydrogen bonds : bond 0.19840 / 13.61 ( 798) hydrogen bonds : angle 7.30765 / 5.05 ( 2298) metal coordination : bond 0.00686 / 0.40 ( 23) metal coordination : angle 4.16446 / 2.83 ( 16) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 576 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 HIS cc_start: 0.8724 (m90) cc_final: 0.8284 (m-70) REVERT: C 228 GLN cc_start: 0.8609 (tt0) cc_final: 0.8284 (tm-30) REVERT: C 316 ASN cc_start: 0.8786 (m-40) cc_final: 0.8540 (m110) REVERT: C 355 TYR cc_start: 0.5715 (m-80) cc_final: 0.5512 (m-10) REVERT: C 423 LEU cc_start: 0.9402 (tt) cc_final: 0.9150 (mt) REVERT: D 81 ASN cc_start: 0.9393 (m-40) cc_final: 0.8878 (t0) REVERT: D 92 GLN cc_start: 0.8977 (tp40) cc_final: 0.8747 (tp-100) REVERT: D 125 GLN cc_start: 0.9544 (tp40) cc_final: 0.9279 (tp-100) REVERT: D 139 ARG cc_start: 0.8979 (mtm180) cc_final: 0.8560 (mmt-90) REVERT: D 140 GLU cc_start: 0.9616 (mt-10) cc_final: 0.9250 (mp0) REVERT: D 145 TYR cc_start: 0.8859 (m-80) cc_final: 0.8627 (m-80) REVERT: I 150 GLN cc_start: 0.8881 (tt0) cc_final: 0.8500 (tt0) REVERT: N 4 LYS cc_start: 0.9219 (mtpt) cc_final: 0.8918 (mttt) REVERT: N 18 GLU cc_start: 0.9328 (pm20) cc_final: 0.9076 (pm20) REVERT: N 36 ILE cc_start: 0.8589 (mm) cc_final: 0.7711 (mm) REVERT: N 54 LYS cc_start: 0.9294 (mmtp) cc_final: 0.8951 (mmmm) REVERT: U 11 LYS cc_start: 0.9305 (mmtt) cc_final: 0.9078 (mptt) REVERT: U 34 GLU cc_start: 0.8429 (tp30) cc_final: 0.7657 (tm-30) REVERT: U 51 GLU cc_start: 0.8236 (mp0) cc_final: 0.7822 (mp0) REVERT: R 27 TRP cc_start: 0.9048 (p-90) cc_final: 0.8786 (p-90) REVERT: R 55 GLU cc_start: 0.9072 (tp30) cc_final: 0.8605 (tm-30) REVERT: R 100 GLU cc_start: 0.8959 (mp0) cc_final: 0.8716 (mp0) REVERT: B 158 ARG cc_start: 0.8749 (mmm-85) cc_final: 0.8506 (mmm-85) REVERT: B 159 LEU cc_start: 0.8940 (tp) cc_final: 0.8347 (tt) REVERT: B 384 GLU cc_start: 0.7746 (mp0) cc_final: 0.7539 (mp0) REVERT: B 590 SER cc_start: 0.9337 (t) cc_final: 0.8896 (m) REVERT: B 741 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8209 (mm-30) REVERT: B 750 THR cc_start: 0.8573 (p) cc_final: 0.8070 (p) REVERT: B 867 LYS cc_start: 0.8787 (mmtp) cc_final: 0.8473 (mmmt) REVERT: B 1105 MET cc_start: 0.7422 (mpp) cc_final: 0.7060 (mpp) REVERT: A 241 CYS cc_start: 0.9149 (t) cc_final: 0.8771 (p) REVERT: A 483 CYS cc_start: 0.8718 (m) cc_final: 0.8437 (t) REVERT: A 554 PHE cc_start: 0.9309 (t80) cc_final: 0.9075 (t80) outliers start: 3 outliers final: 0 residues processed: 579 average time/residue: 0.1382 time to fit residues: 123.6255 Evaluate side-chains 387 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 30.0000 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 71 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 236 ASN D 77 ASN D 137 HIS I 177 HIS ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 ASN U 31 GLN ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 ASN B 810 ASN B 905 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.122100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.088033 restraints weight = 61394.074| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 6.09 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 21240 Z= 0.222 Angle : 0.696 12.131 28717 Z= 0.357 Chirality : 0.046 0.193 3238 Planarity : 0.004 0.042 3679 Dihedral : 6.633 87.921 2849 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.01 % Allowed : 11.65 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.25 (0.16), residues: 2590 helix: 1.18 (0.20), residues: 723 sheet: -1.17 (0.21), residues: 620 loop : -1.88 (0.16), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1080 TYR 0.023 0.002 TYR B 91 PHE 0.019 0.002 PHE B 140 TRP 0.014 0.002 TRP C 386 HIS 0.007 0.001 HIS I 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.22 (21216) covalent geometry : angle 0.68471 / 0.36 (28699) SS BOND : bond 0.00012 / 0.01 ( 1) SS BOND : angle 0.43308 / 0.24 ( 2) hydrogen bonds : bond 0.04499 / 3.08 ( 798) hydrogen bonds : angle 5.41056 / 3.75 ( 2298) metal coordination : bond 0.01214 / 0.57 ( 23) metal coordination : angle 5.38256 / 3.86 ( 16) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 403 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 MET cc_start: 0.9025 (tpp) cc_final: 0.8774 (tpp) REVERT: C 198 GLN cc_start: 0.7566 (pp30) cc_final: 0.6813 (pp30) REVERT: C 199 LEU cc_start: 0.8464 (mp) cc_final: 0.7957 (mt) REVERT: C 228 GLN cc_start: 0.8361 (tt0) cc_final: 0.7811 (tm-30) REVERT: C 316 ASN cc_start: 0.9080 (m-40) cc_final: 0.8688 (m110) REVERT: C 355 TYR cc_start: 0.5287 (m-10) cc_final: 0.5030 (m-10) REVERT: D 36 THR cc_start: 0.9562 (m) cc_final: 0.9250 (p) REVERT: D 92 GLN cc_start: 0.9122 (tp40) cc_final: 0.8872 (tp-100) REVERT: D 125 GLN cc_start: 0.9589 (tp40) cc_final: 0.9265 (tm-30) REVERT: D 145 TYR cc_start: 0.9027 (m-80) cc_final: 0.8534 (m-80) REVERT: I 149 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8519 (m-40) REVERT: I 150 GLN cc_start: 0.8741 (tt0) cc_final: 0.8312 (tt0) REVERT: N 4 LYS cc_start: 0.9051 (mtpt) cc_final: 0.8663 (mttt) REVERT: N 36 ILE cc_start: 0.8450 (mm) cc_final: 0.7914 (mm) REVERT: N 44 ILE cc_start: 0.9194 (mt) cc_final: 0.8799 (mm) REVERT: N 54 LYS cc_start: 0.9345 (mmtp) cc_final: 0.8877 (mmmm) REVERT: U 34 GLU cc_start: 0.8750 (tp30) cc_final: 0.7971 (tm-30) REVERT: R 55 GLU cc_start: 0.9247 (tp30) cc_final: 0.8692 (tm-30) REVERT: B 47 GLU cc_start: 0.9313 (pm20) cc_final: 0.8987 (pm20) REVERT: B 130 MET cc_start: 0.7964 (ppp) cc_final: 0.7620 (ppp) REVERT: B 158 ARG cc_start: 0.8845 (mmm-85) cc_final: 0.8424 (mmm-85) REVERT: B 159 LEU cc_start: 0.8842 (tp) cc_final: 0.8131 (tt) REVERT: B 330 ASP cc_start: 0.8324 (m-30) cc_final: 0.7849 (m-30) REVERT: B 410 LEU cc_start: 0.8626 (mt) cc_final: 0.8327 (pt) REVERT: B 590 SER cc_start: 0.9203 (t) cc_final: 0.8798 (m) REVERT: B 608 ASP cc_start: 0.8850 (p0) cc_final: 0.8535 (p0) REVERT: B 741 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8279 (mm-30) REVERT: B 750 THR cc_start: 0.8082 (p) cc_final: 0.7624 (p) REVERT: B 786 VAL cc_start: 0.9340 (t) cc_final: 0.9065 (m) REVERT: B 958 GLU cc_start: 0.8554 (tp30) cc_final: 0.8029 (tp30) REVERT: B 1080 ARG cc_start: 0.7867 (ttp80) cc_final: 0.7485 (ttp80) REVERT: A 107 ARG cc_start: 0.9219 (mmm160) cc_final: 0.8930 (tmm160) REVERT: A 187 MET cc_start: 0.9346 (ptt) cc_final: 0.9033 (ppp) REVERT: A 241 CYS cc_start: 0.9009 (t) cc_final: 0.8628 (p) REVERT: A 293 GLN cc_start: 0.8812 (mm110) cc_final: 0.8546 (mm110) REVERT: A 437 MET cc_start: 0.9493 (mmm) cc_final: 0.9234 (tmm) REVERT: A 483 CYS cc_start: 0.8719 (m) cc_final: 0.8519 (t) REVERT: A 494 MET cc_start: 0.9420 (mmt) cc_final: 0.9136 (mmt) REVERT: A 547 MET cc_start: 0.9584 (tpt) cc_final: 0.9233 (tpt) REVERT: A 554 PHE cc_start: 0.9396 (t80) cc_final: 0.9142 (t80) outliers start: 46 outliers final: 25 residues processed: 426 average time/residue: 0.1454 time to fit residues: 96.4784 Evaluate side-chains 377 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 351 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 141 TRP Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 676 VAL Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain A residue 260 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 242 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 2 optimal weight: 50.0000 chunk 184 optimal weight: 0.0670 chunk 117 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 overall best weight: 2.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 77 ASN I 147 GLN ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.120676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086409 restraints weight = 60802.054| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 6.04 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21240 Z= 0.145 Angle : 0.635 14.981 28717 Z= 0.316 Chirality : 0.043 0.214 3238 Planarity : 0.004 0.043 3679 Dihedral : 6.123 89.197 2849 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.01 % Allowed : 14.02 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.19 (0.16), residues: 2590 helix: 1.21 (0.20), residues: 734 sheet: -1.16 (0.20), residues: 650 loop : -1.86 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 42 TYR 0.013 0.001 TYR B 91 PHE 0.014 0.001 PHE C 150 TRP 0.013 0.001 TRP R 33 HIS 0.005 0.001 HIS I 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (21216) covalent geometry : angle 0.62753 / 0.32 (28699) SS BOND : bond 0.00035 / 0.02 ( 1) SS BOND : angle 0.34812 / 0.19 ( 2) hydrogen bonds : bond 0.03981 / 2.74 ( 798) hydrogen bonds : angle 4.99614 / 3.45 ( 2298) metal coordination : bond 0.00861 / 0.44 ( 23) metal coordination : angle 4.27914 / 3.12 ( 16) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 376 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 228 GLN cc_start: 0.8315 (tt0) cc_final: 0.7817 (tm-30) REVERT: C 306 GLN cc_start: 0.8900 (mt0) cc_final: 0.8625 (mt0) REVERT: D 36 THR cc_start: 0.9548 (m) cc_final: 0.9216 (p) REVERT: D 92 GLN cc_start: 0.9112 (tp40) cc_final: 0.8850 (tp-100) REVERT: D 125 GLN cc_start: 0.9576 (tp40) cc_final: 0.9271 (tp-100) REVERT: D 139 ARG cc_start: 0.8887 (mtm180) cc_final: 0.8328 (mmp80) REVERT: D 141 TRP cc_start: 0.8895 (OUTLIER) cc_final: 0.8600 (m100) REVERT: D 144 LYS cc_start: 0.9524 (ptpp) cc_final: 0.9278 (ptpp) REVERT: D 145 TYR cc_start: 0.8961 (m-80) cc_final: 0.8294 (m-80) REVERT: I 150 GLN cc_start: 0.8733 (tt0) cc_final: 0.8282 (tt0) REVERT: N 4 LYS cc_start: 0.9033 (mtpt) cc_final: 0.8693 (mtpp) REVERT: N 44 ILE cc_start: 0.9165 (mt) cc_final: 0.8763 (mm) REVERT: N 54 LYS cc_start: 0.9336 (mmtp) cc_final: 0.8832 (mmmm) REVERT: U 34 GLU cc_start: 0.8720 (tp30) cc_final: 0.8029 (tm-30) REVERT: U 41 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: R 55 GLU cc_start: 0.9183 (tp30) cc_final: 0.8664 (tm-30) REVERT: B 130 MET cc_start: 0.8157 (ppp) cc_final: 0.7897 (ppp) REVERT: B 158 ARG cc_start: 0.8871 (mmm-85) cc_final: 0.8530 (mmm-85) REVERT: B 159 LEU cc_start: 0.8808 (tp) cc_final: 0.8371 (tp) REVERT: B 277 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8210 (mm-30) REVERT: B 312 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8208 (tm-30) REVERT: B 330 ASP cc_start: 0.8298 (m-30) cc_final: 0.7871 (m-30) REVERT: B 521 ILE cc_start: 0.8714 (mm) cc_final: 0.8509 (tp) REVERT: B 590 SER cc_start: 0.9088 (t) cc_final: 0.8715 (m) REVERT: B 741 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8329 (mm-30) REVERT: B 750 THR cc_start: 0.8070 (p) cc_final: 0.7657 (p) REVERT: B 786 VAL cc_start: 0.9391 (t) cc_final: 0.9119 (m) REVERT: B 811 GLU cc_start: 0.8790 (tt0) cc_final: 0.8567 (tt0) REVERT: B 867 LYS cc_start: 0.8671 (tppt) cc_final: 0.8358 (mmmt) REVERT: B 873 MET cc_start: 0.8437 (mtm) cc_final: 0.7776 (mtm) REVERT: B 958 GLU cc_start: 0.8690 (tp30) cc_final: 0.8250 (tp30) REVERT: B 1062 ILE cc_start: 0.8727 (tp) cc_final: 0.8487 (pt) REVERT: B 1105 MET cc_start: 0.7686 (mpp) cc_final: 0.7384 (mmm) REVERT: A 107 ARG cc_start: 0.9270 (mmm160) cc_final: 0.8948 (tmm160) REVERT: A 173 MET cc_start: 0.9715 (ttp) cc_final: 0.9281 (tmm) REVERT: A 187 MET cc_start: 0.9335 (ptt) cc_final: 0.9031 (ppp) REVERT: A 241 CYS cc_start: 0.9031 (t) cc_final: 0.8638 (p) REVERT: A 293 GLN cc_start: 0.8843 (mm110) cc_final: 0.8556 (mm110) REVERT: A 437 MET cc_start: 0.9539 (mmm) cc_final: 0.9254 (tmm) REVERT: A 483 CYS cc_start: 0.8654 (m) cc_final: 0.8256 (t) REVERT: A 494 MET cc_start: 0.9418 (mmt) cc_final: 0.8894 (mmt) REVERT: A 554 PHE cc_start: 0.9374 (t80) cc_final: 0.9107 (t80) outliers start: 46 outliers final: 28 residues processed: 407 average time/residue: 0.1347 time to fit residues: 86.2027 Evaluate side-chains 382 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 352 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 141 TRP Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain U residue 41 GLN Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain A residue 93 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 102 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 39 optimal weight: 0.4980 chunk 22 optimal weight: 6.9990 chunk 2 optimal weight: 40.0000 chunk 6 optimal weight: 6.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 55 HIS D 77 ASN ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN B 845 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.118727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.084233 restraints weight = 61228.722| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 5.86 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21240 Z= 0.191 Angle : 0.637 9.843 28717 Z= 0.326 Chirality : 0.044 0.183 3238 Planarity : 0.004 0.043 3679 Dihedral : 5.982 88.965 2849 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.24 % Allowed : 15.42 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.20 (0.16), residues: 2590 helix: 1.25 (0.20), residues: 732 sheet: -1.14 (0.20), residues: 632 loop : -1.90 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1080 TYR 0.014 0.001 TYR B 58 PHE 0.021 0.001 PHE B 799 TRP 0.016 0.001 TRP R 33 HIS 0.010 0.001 HIS C 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (21216) covalent geometry : angle 0.62962 / 0.33 (28699) SS BOND : bond 0.00098 / 0.05 ( 1) SS BOND : angle 0.24270 / 0.14 ( 2) hydrogen bonds : bond 0.03971 / 2.71 ( 798) hydrogen bonds : angle 4.89756 / 3.39 ( 2298) metal coordination : bond 0.01184 / 0.56 ( 23) metal coordination : angle 4.26013 / 3.06 ( 16) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 361 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 198 GLN cc_start: 0.7704 (pp30) cc_final: 0.6910 (pp30) REVERT: C 228 GLN cc_start: 0.8465 (tt0) cc_final: 0.7891 (tm-30) REVERT: C 306 GLN cc_start: 0.8994 (mt0) cc_final: 0.8663 (mt0) REVERT: C 330 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7355 (mp0) REVERT: C 358 GLU cc_start: 0.8723 (mp0) cc_final: 0.8430 (mp0) REVERT: C 422 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9133 (mp) REVERT: D 32 HIS cc_start: 0.8681 (m90) cc_final: 0.8307 (t-170) REVERT: D 36 THR cc_start: 0.9539 (m) cc_final: 0.9223 (p) REVERT: D 92 GLN cc_start: 0.9121 (tp40) cc_final: 0.8830 (tp-100) REVERT: D 125 GLN cc_start: 0.9580 (tp40) cc_final: 0.9240 (tm-30) REVERT: D 139 ARG cc_start: 0.8961 (mtm180) cc_final: 0.8444 (mmp80) REVERT: D 141 TRP cc_start: 0.8926 (OUTLIER) cc_final: 0.8703 (m100) REVERT: D 144 LYS cc_start: 0.9503 (ptpp) cc_final: 0.9289 (ptpp) REVERT: D 145 TYR cc_start: 0.8952 (m-80) cc_final: 0.8343 (m-80) REVERT: I 150 GLN cc_start: 0.8718 (tt0) cc_final: 0.8237 (tt0) REVERT: N 4 LYS cc_start: 0.9029 (mtpt) cc_final: 0.8601 (mttt) REVERT: N 44 ILE cc_start: 0.9122 (mt) cc_final: 0.8723 (mm) REVERT: N 54 LYS cc_start: 0.9311 (mmtp) cc_final: 0.8855 (mmmm) REVERT: U 34 GLU cc_start: 0.8713 (tp30) cc_final: 0.8060 (tm-30) REVERT: U 41 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7355 (mp10) REVERT: R 50 MET cc_start: 0.9392 (mmm) cc_final: 0.9190 (mmm) REVERT: R 55 GLU cc_start: 0.9261 (tp30) cc_final: 0.8724 (tm-30) REVERT: B 130 MET cc_start: 0.8322 (ppp) cc_final: 0.8042 (ppp) REVERT: B 158 ARG cc_start: 0.8857 (mmm-85) cc_final: 0.8494 (mmm-85) REVERT: B 218 MET cc_start: 0.8790 (tpp) cc_final: 0.8202 (ttp) REVERT: B 277 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8337 (mm-30) REVERT: B 312 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8354 (tm-30) REVERT: B 330 ASP cc_start: 0.8272 (m-30) cc_final: 0.7957 (m-30) REVERT: B 534 MET cc_start: 0.8611 (tpp) cc_final: 0.8409 (mmp) REVERT: B 590 SER cc_start: 0.8985 (t) cc_final: 0.8617 (m) REVERT: B 608 ASP cc_start: 0.8898 (p0) cc_final: 0.8649 (p0) REVERT: B 679 MET cc_start: 0.7987 (ppp) cc_final: 0.7672 (ppp) REVERT: B 741 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8242 (mm-30) REVERT: B 750 THR cc_start: 0.8104 (p) cc_final: 0.7663 (p) REVERT: B 786 VAL cc_start: 0.9313 (t) cc_final: 0.9003 (m) REVERT: B 873 MET cc_start: 0.8540 (mtm) cc_final: 0.8050 (mtm) REVERT: B 1105 MET cc_start: 0.7809 (mpp) cc_final: 0.7581 (mpp) REVERT: A 107 ARG cc_start: 0.9349 (mmm160) cc_final: 0.9035 (tmm160) REVERT: A 173 MET cc_start: 0.9740 (ttp) cc_final: 0.9334 (tmm) REVERT: A 241 CYS cc_start: 0.9063 (t) cc_final: 0.8702 (p) REVERT: A 437 MET cc_start: 0.9542 (mmm) cc_final: 0.9282 (tmm) REVERT: A 483 CYS cc_start: 0.8721 (m) cc_final: 0.8197 (t) REVERT: A 492 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.9101 (mp0) REVERT: A 494 MET cc_start: 0.9509 (mmt) cc_final: 0.8606 (mmt) REVERT: A 554 PHE cc_start: 0.9404 (t80) cc_final: 0.9143 (t80) REVERT: A 704 MET cc_start: 0.7036 (tpp) cc_final: 0.6682 (tpt) outliers start: 74 outliers final: 45 residues processed: 408 average time/residue: 0.1419 time to fit residues: 91.0654 Evaluate side-chains 399 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 350 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 141 TRP Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain U residue 41 GLN Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1014 MET Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 669 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 225 optimal weight: 0.0870 chunk 229 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 161 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 77 ASN ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.118387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.084022 restraints weight = 60449.496| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 5.90 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21240 Z= 0.174 Angle : 0.627 8.853 28717 Z= 0.317 Chirality : 0.044 0.219 3238 Planarity : 0.004 0.048 3679 Dihedral : 5.803 89.220 2849 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.29 % Allowed : 16.21 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.18 (0.16), residues: 2590 helix: 1.28 (0.20), residues: 734 sheet: -1.13 (0.20), residues: 632 loop : -1.91 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1080 TYR 0.016 0.001 TYR D 60 PHE 0.018 0.001 PHE B 799 TRP 0.013 0.001 TRP C 415 HIS 0.005 0.001 HIS I 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (21216) covalent geometry : angle 0.61999 / 0.32 (28699) SS BOND : bond 0.00002 / 0.00 ( 1) SS BOND : angle 0.00926 / 0.01 ( 2) hydrogen bonds : bond 0.03846 / 2.62 ( 798) hydrogen bonds : angle 4.77252 / 3.30 ( 2298) metal coordination : bond 0.01095 / 0.54 ( 23) metal coordination : angle 4.01675 / 2.86 ( 16) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 368 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 MET cc_start: 0.9037 (tpp) cc_final: 0.8746 (tpp) REVERT: C 198 GLN cc_start: 0.7680 (pp30) cc_final: 0.6873 (pp30) REVERT: C 228 GLN cc_start: 0.8456 (tt0) cc_final: 0.7965 (tm-30) REVERT: C 306 GLN cc_start: 0.9022 (mt0) cc_final: 0.8650 (mt0) REVERT: C 330 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7290 (mp0) REVERT: C 358 GLU cc_start: 0.8685 (mp0) cc_final: 0.8395 (mp0) REVERT: C 422 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9111 (mp) REVERT: D 32 HIS cc_start: 0.8680 (m90) cc_final: 0.8400 (t-170) REVERT: D 34 GLN cc_start: 0.8996 (tt0) cc_final: 0.8521 (tp-100) REVERT: D 36 THR cc_start: 0.9515 (m) cc_final: 0.9205 (p) REVERT: D 46 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8250 (mm-40) REVERT: D 52 LEU cc_start: 0.8881 (mp) cc_final: 0.8387 (mp) REVERT: D 92 GLN cc_start: 0.9092 (tp40) cc_final: 0.8791 (tp-100) REVERT: D 125 GLN cc_start: 0.9574 (tp40) cc_final: 0.9239 (tm-30) REVERT: D 141 TRP cc_start: 0.8902 (OUTLIER) cc_final: 0.8694 (m100) REVERT: D 143 GLN cc_start: 0.9321 (tt0) cc_final: 0.9057 (mt0) REVERT: D 144 LYS cc_start: 0.9514 (ptpp) cc_final: 0.9293 (ptpp) REVERT: D 145 TYR cc_start: 0.8962 (m-80) cc_final: 0.8342 (m-80) REVERT: I 150 GLN cc_start: 0.8748 (tt0) cc_final: 0.8224 (tt0) REVERT: N 1 MET cc_start: 0.8506 (mtp) cc_final: 0.8209 (mtm) REVERT: N 4 LYS cc_start: 0.9062 (mtpt) cc_final: 0.8725 (mtpp) REVERT: N 44 ILE cc_start: 0.9118 (mt) cc_final: 0.8714 (mm) REVERT: N 54 LYS cc_start: 0.9296 (mmtp) cc_final: 0.8844 (mmmm) REVERT: U 4 PHE cc_start: 0.9103 (m-10) cc_final: 0.8719 (m-80) REVERT: U 34 GLU cc_start: 0.8674 (tp30) cc_final: 0.7968 (tm-30) REVERT: R 55 GLU cc_start: 0.9216 (tp30) cc_final: 0.8672 (tm-30) REVERT: B 130 MET cc_start: 0.8468 (ppp) cc_final: 0.8212 (ppp) REVERT: B 158 ARG cc_start: 0.8861 (mmm-85) cc_final: 0.8505 (mmm-85) REVERT: B 218 MET cc_start: 0.8824 (tpp) cc_final: 0.8252 (ttp) REVERT: B 260 CYS cc_start: 0.8402 (t) cc_final: 0.8149 (t) REVERT: B 275 ASP cc_start: 0.8473 (p0) cc_final: 0.8201 (p0) REVERT: B 312 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8484 (tm-30) REVERT: B 315 THR cc_start: 0.8142 (p) cc_final: 0.7826 (p) REVERT: B 330 ASP cc_start: 0.8366 (m-30) cc_final: 0.8050 (m-30) REVERT: B 366 ASP cc_start: 0.8709 (p0) cc_final: 0.8506 (p0) REVERT: B 534 MET cc_start: 0.8705 (tpp) cc_final: 0.8491 (mmp) REVERT: B 590 SER cc_start: 0.8932 (t) cc_final: 0.8705 (m) REVERT: B 608 ASP cc_start: 0.8933 (p0) cc_final: 0.8700 (p0) REVERT: B 679 MET cc_start: 0.8043 (ppp) cc_final: 0.7732 (ppp) REVERT: B 741 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8232 (mm-30) REVERT: B 750 THR cc_start: 0.8097 (p) cc_final: 0.7626 (p) REVERT: B 786 VAL cc_start: 0.9304 (t) cc_final: 0.9012 (m) REVERT: B 873 MET cc_start: 0.8520 (mtm) cc_final: 0.8062 (mtm) REVERT: B 1105 MET cc_start: 0.7839 (mpp) cc_final: 0.7611 (mpp) REVERT: A 107 ARG cc_start: 0.9361 (mmm160) cc_final: 0.9039 (tmm160) REVERT: A 173 MET cc_start: 0.9745 (ttp) cc_final: 0.9243 (tmm) REVERT: A 241 CYS cc_start: 0.9052 (t) cc_final: 0.8693 (p) REVERT: A 437 MET cc_start: 0.9494 (mmm) cc_final: 0.9260 (tmm) REVERT: A 483 CYS cc_start: 0.8704 (m) cc_final: 0.8078 (t) REVERT: A 492 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.8872 (mp0) REVERT: A 494 MET cc_start: 0.9476 (mmt) cc_final: 0.8623 (mmt) REVERT: A 554 PHE cc_start: 0.9392 (t80) cc_final: 0.9139 (t80) REVERT: A 704 MET cc_start: 0.7263 (tpp) cc_final: 0.6873 (tpt) outliers start: 75 outliers final: 53 residues processed: 420 average time/residue: 0.1388 time to fit residues: 91.3574 Evaluate side-chains 405 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 349 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 141 TRP Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain U residue 41 GLN Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 557 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 75 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 HIS ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.114828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.080358 restraints weight = 61223.703| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 5.90 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 21240 Z= 0.265 Angle : 0.699 12.076 28717 Z= 0.356 Chirality : 0.046 0.194 3238 Planarity : 0.004 0.048 3679 Dihedral : 5.971 88.780 2849 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.94 % Allowed : 17.30 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.36 (0.16), residues: 2590 helix: 1.10 (0.20), residues: 736 sheet: -1.31 (0.20), residues: 639 loop : -1.95 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1080 TYR 0.021 0.002 TYR C 59 PHE 0.023 0.002 PHE A 48 TRP 0.017 0.002 TRP C 380 HIS 0.006 0.001 HIS I 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.26 (21216) covalent geometry : angle 0.68957 / 0.36 (28699) SS BOND : bond 0.00032 / 0.02 ( 1) SS BOND : angle 0.49694 / 0.26 ( 2) hydrogen bonds : bond 0.04346 / 2.97 ( 798) hydrogen bonds : angle 4.90658 / 3.40 ( 2298) metal coordination : bond 0.01695 / 0.79 ( 23) metal coordination : angle 4.97682 / 3.40 ( 16) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 354 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 MET cc_start: 0.8979 (tpp) cc_final: 0.8644 (tpp) REVERT: C 185 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8780 (mm) REVERT: C 198 GLN cc_start: 0.7726 (pp30) cc_final: 0.6906 (pp30) REVERT: C 228 GLN cc_start: 0.8608 (tt0) cc_final: 0.8052 (tm-30) REVERT: C 306 GLN cc_start: 0.9001 (mt0) cc_final: 0.8777 (mt0) REVERT: C 330 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7314 (mp0) REVERT: C 358 GLU cc_start: 0.8708 (mp0) cc_final: 0.8400 (mp0) REVERT: C 422 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9124 (mp) REVERT: D 36 THR cc_start: 0.9532 (m) cc_final: 0.9241 (p) REVERT: D 125 GLN cc_start: 0.9570 (tp40) cc_final: 0.9236 (tm-30) REVERT: D 139 ARG cc_start: 0.9070 (mtm180) cc_final: 0.8495 (mmp80) REVERT: I 150 GLN cc_start: 0.8814 (tt0) cc_final: 0.8272 (tt0) REVERT: N 4 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8806 (mtpp) REVERT: N 44 ILE cc_start: 0.9155 (mt) cc_final: 0.8766 (mm) REVERT: N 54 LYS cc_start: 0.9308 (mmtp) cc_final: 0.8880 (mmmm) REVERT: U 4 PHE cc_start: 0.9055 (m-10) cc_final: 0.8654 (m-80) REVERT: U 34 GLU cc_start: 0.8708 (tp30) cc_final: 0.8018 (tm-30) REVERT: U 41 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7362 (mp10) REVERT: U 51 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7870 (pm20) REVERT: B 1 MET cc_start: 0.8023 (mmm) cc_final: 0.7592 (mmp) REVERT: B 130 MET cc_start: 0.8485 (ppp) cc_final: 0.8172 (ppp) REVERT: B 158 ARG cc_start: 0.8836 (mmm-85) cc_final: 0.8499 (mmm-85) REVERT: B 275 ASP cc_start: 0.8565 (p0) cc_final: 0.8269 (p0) REVERT: B 277 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8372 (mm-30) REVERT: B 312 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8509 (tm-30) REVERT: B 330 ASP cc_start: 0.8521 (m-30) cc_final: 0.8183 (m-30) REVERT: B 366 ASP cc_start: 0.8785 (p0) cc_final: 0.8534 (p0) REVERT: B 403 ASP cc_start: 0.8541 (m-30) cc_final: 0.8296 (t0) REVERT: B 608 ASP cc_start: 0.9025 (p0) cc_final: 0.8821 (p0) REVERT: B 741 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8202 (mm-30) REVERT: B 750 THR cc_start: 0.7942 (p) cc_final: 0.7458 (p) REVERT: B 786 VAL cc_start: 0.9320 (t) cc_final: 0.9041 (m) REVERT: B 1039 LEU cc_start: 0.9287 (tt) cc_final: 0.9082 (tt) REVERT: B 1050 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.6752 (tp) REVERT: B 1105 MET cc_start: 0.8018 (mpp) cc_final: 0.7576 (mmt) REVERT: A 107 ARG cc_start: 0.9385 (mmm160) cc_final: 0.9092 (tmm160) REVERT: A 173 MET cc_start: 0.9767 (ttp) cc_final: 0.9247 (tmm) REVERT: A 241 CYS cc_start: 0.9030 (t) cc_final: 0.8733 (p) REVERT: A 492 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.8913 (mp0) REVERT: A 494 MET cc_start: 0.9486 (mmt) cc_final: 0.8720 (mmt) REVERT: A 542 HIS cc_start: 0.9102 (m-70) cc_final: 0.8729 (p-80) REVERT: A 704 MET cc_start: 0.7489 (tpp) cc_final: 0.7181 (tpt) outliers start: 90 outliers final: 63 residues processed: 414 average time/residue: 0.1389 time to fit residues: 90.2703 Evaluate side-chains 393 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 325 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain U residue 41 GLN Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 521 ILE Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 616 LEU Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1014 MET Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain B residue 1050 LEU Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 557 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 219 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 221 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 209 optimal weight: 0.6980 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 353 HIS D 55 HIS D 77 ASN ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1055 GLN ** A 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.116565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.082404 restraints weight = 61203.020| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 5.80 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21240 Z= 0.166 Angle : 0.663 12.342 28717 Z= 0.331 Chirality : 0.045 0.372 3238 Planarity : 0.004 0.058 3679 Dihedral : 5.718 89.784 2849 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.02 % Allowed : 19.40 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.26 (0.16), residues: 2590 helix: 1.19 (0.20), residues: 735 sheet: -1.25 (0.20), residues: 634 loop : -1.90 (0.16), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1080 TYR 0.015 0.001 TYR C 363 PHE 0.018 0.001 PHE B 799 TRP 0.012 0.001 TRP B1047 HIS 0.005 0.001 HIS I 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (21216) covalent geometry : angle 0.65596 / 0.33 (28699) SS BOND : bond 0.00037 / 0.02 ( 1) SS BOND : angle 0.21582 / 0.11 ( 2) hydrogen bonds : bond 0.03850 / 2.64 ( 798) hydrogen bonds : angle 4.73902 / 3.30 ( 2298) metal coordination : bond 0.01013 / 0.46 ( 23) metal coordination : angle 4.13398 / 2.79 ( 16) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 350 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 TYR cc_start: 0.6853 (p90) cc_final: 0.6603 (p90) REVERT: C 185 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8711 (mm) REVERT: C 198 GLN cc_start: 0.7642 (pp30) cc_final: 0.6856 (pp30) REVERT: C 228 GLN cc_start: 0.8558 (tt0) cc_final: 0.8008 (tm-30) REVERT: C 306 GLN cc_start: 0.9014 (mt0) cc_final: 0.8762 (mt0) REVERT: C 330 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7281 (mp0) REVERT: C 422 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9080 (mp) REVERT: D 34 GLN cc_start: 0.9032 (tt0) cc_final: 0.8584 (tp-100) REVERT: D 36 THR cc_start: 0.9490 (m) cc_final: 0.9201 (p) REVERT: D 52 LEU cc_start: 0.8838 (mp) cc_final: 0.8388 (mt) REVERT: D 66 LYS cc_start: 0.9364 (ttmm) cc_final: 0.9119 (ttmm) REVERT: D 125 GLN cc_start: 0.9571 (tp40) cc_final: 0.9187 (tp-100) REVERT: D 139 ARG cc_start: 0.8926 (mtm180) cc_final: 0.8429 (mmp80) REVERT: D 145 TYR cc_start: 0.8898 (m-80) cc_final: 0.8457 (m-80) REVERT: I 150 GLN cc_start: 0.8813 (tt0) cc_final: 0.8257 (tt0) REVERT: N 1 MET cc_start: 0.8534 (mtp) cc_final: 0.8227 (mtm) REVERT: N 4 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8743 (mtpp) REVERT: N 44 ILE cc_start: 0.9111 (mt) cc_final: 0.8724 (mm) REVERT: N 58 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8625 (p0) REVERT: U 4 PHE cc_start: 0.9062 (m-10) cc_final: 0.8630 (m-80) REVERT: U 34 GLU cc_start: 0.8682 (tp30) cc_final: 0.8005 (tm-30) REVERT: R 55 GLU cc_start: 0.9283 (tp30) cc_final: 0.8655 (tm-30) REVERT: B 1 MET cc_start: 0.7966 (mmm) cc_final: 0.7516 (mmp) REVERT: B 130 MET cc_start: 0.8531 (ppp) cc_final: 0.8300 (ppp) REVERT: B 158 ARG cc_start: 0.8835 (mmm-85) cc_final: 0.8491 (mmm-85) REVERT: B 218 MET cc_start: 0.8742 (tpp) cc_final: 0.8219 (ttm) REVERT: B 275 ASP cc_start: 0.8621 (p0) cc_final: 0.8354 (p0) REVERT: B 312 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8531 (tm-30) REVERT: B 315 THR cc_start: 0.8245 (p) cc_final: 0.7920 (p) REVERT: B 330 ASP cc_start: 0.8422 (m-30) cc_final: 0.8086 (m-30) REVERT: B 366 ASP cc_start: 0.8780 (p0) cc_final: 0.8500 (p0) REVERT: B 403 ASP cc_start: 0.8519 (m-30) cc_final: 0.8275 (t0) REVERT: B 534 MET cc_start: 0.8661 (mmp) cc_final: 0.8379 (mmp) REVERT: B 608 ASP cc_start: 0.8981 (p0) cc_final: 0.8764 (p0) REVERT: B 741 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8221 (mm-30) REVERT: B 750 THR cc_start: 0.7957 (p) cc_final: 0.7514 (p) REVERT: B 786 VAL cc_start: 0.9290 (t) cc_final: 0.9000 (m) REVERT: B 1096 SER cc_start: 0.9180 (p) cc_final: 0.8950 (p) REVERT: B 1105 MET cc_start: 0.8013 (mpp) cc_final: 0.7758 (mpp) REVERT: A 107 ARG cc_start: 0.9398 (mmm160) cc_final: 0.9111 (tmm160) REVERT: A 173 MET cc_start: 0.9755 (ttp) cc_final: 0.9279 (tmm) REVERT: A 241 CYS cc_start: 0.9048 (t) cc_final: 0.8653 (p) REVERT: A 456 ASP cc_start: 0.9248 (m-30) cc_final: 0.8770 (t0) REVERT: A 483 CYS cc_start: 0.8899 (m) cc_final: 0.7947 (t) REVERT: A 492 GLU cc_start: 0.9306 (mt-10) cc_final: 0.9082 (mp0) REVERT: A 494 MET cc_start: 0.9457 (mmt) cc_final: 0.8575 (mmt) REVERT: A 542 HIS cc_start: 0.9102 (m-70) cc_final: 0.8720 (p-80) REVERT: A 704 MET cc_start: 0.7678 (tpp) cc_final: 0.7280 (tpp) REVERT: A 720 TYR cc_start: 0.8365 (m-10) cc_final: 0.8121 (m-80) outliers start: 69 outliers final: 55 residues processed: 395 average time/residue: 0.1456 time to fit residues: 90.4304 Evaluate side-chains 403 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 345 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 360 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain U residue 41 GLN Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 425 LEU Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 625 ASP Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 557 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 155 optimal weight: 3.9990 chunk 104 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 0.3980 chunk 69 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 92 optimal weight: 0.0270 overall best weight: 1.8844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 77 ASN ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN A 399 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.117920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.083982 restraints weight = 60441.634| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 5.79 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21240 Z= 0.124 Angle : 0.646 16.166 28717 Z= 0.320 Chirality : 0.044 0.333 3238 Planarity : 0.004 0.052 3679 Dihedral : 5.438 87.895 2849 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.89 % Allowed : 19.62 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.12 (0.16), residues: 2590 helix: 1.32 (0.20), residues: 735 sheet: -1.11 (0.20), residues: 635 loop : -1.85 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1080 TYR 0.012 0.001 TYR C 59 PHE 0.015 0.001 PHE B 799 TRP 0.014 0.001 TRP C 415 HIS 0.004 0.001 HIS I 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (21216) covalent geometry : angle 0.64041 / 0.32 (28699) SS BOND : bond 0.00041 / 0.02 ( 1) SS BOND : angle 0.36636 / 0.19 ( 2) hydrogen bonds : bond 0.03476 / 2.40 ( 798) hydrogen bonds : angle 4.55590 / 3.18 ( 2298) metal coordination : bond 0.00677 / 0.34 ( 23) metal coordination : angle 3.54792 / 2.40 ( 16) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 366 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 MET cc_start: 0.8940 (tpp) cc_final: 0.8524 (tpp) REVERT: C 185 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8716 (mm) REVERT: C 198 GLN cc_start: 0.7599 (pp30) cc_final: 0.6897 (pp30) REVERT: C 228 GLN cc_start: 0.8445 (tt0) cc_final: 0.7993 (tm-30) REVERT: C 262 ARG cc_start: 0.9073 (ttm-80) cc_final: 0.8700 (ttm-80) REVERT: C 306 GLN cc_start: 0.9007 (mt0) cc_final: 0.8707 (mt0) REVERT: C 330 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7236 (mp0) REVERT: C 422 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9062 (mp) REVERT: D 36 THR cc_start: 0.9462 (m) cc_final: 0.9182 (p) REVERT: D 55 HIS cc_start: 0.9013 (m170) cc_final: 0.8805 (m-70) REVERT: D 125 GLN cc_start: 0.9573 (tp40) cc_final: 0.9190 (tp-100) REVERT: D 139 ARG cc_start: 0.8894 (mtm180) cc_final: 0.8669 (ttm110) REVERT: D 145 TYR cc_start: 0.8927 (m-80) cc_final: 0.8546 (m-80) REVERT: I 150 GLN cc_start: 0.8804 (tt0) cc_final: 0.8254 (tt0) REVERT: N 1 MET cc_start: 0.8468 (mtp) cc_final: 0.8142 (mtm) REVERT: N 4 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8730 (mtpp) REVERT: N 44 ILE cc_start: 0.9083 (mt) cc_final: 0.8677 (mm) REVERT: U 34 GLU cc_start: 0.8680 (tp30) cc_final: 0.8003 (tm-30) REVERT: R 55 GLU cc_start: 0.9260 (tp30) cc_final: 0.8641 (tm-30) REVERT: B 1 MET cc_start: 0.8029 (mmm) cc_final: 0.7636 (mmp) REVERT: B 130 MET cc_start: 0.8552 (ppp) cc_final: 0.8335 (ppp) REVERT: B 158 ARG cc_start: 0.8842 (mmm-85) cc_final: 0.8495 (mmm-85) REVERT: B 218 MET cc_start: 0.8690 (tpp) cc_final: 0.8186 (ttm) REVERT: B 275 ASP cc_start: 0.8699 (p0) cc_final: 0.8357 (p0) REVERT: B 277 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8375 (mm-30) REVERT: B 312 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8499 (tm-30) REVERT: B 315 THR cc_start: 0.8034 (p) cc_final: 0.7668 (p) REVERT: B 366 ASP cc_start: 0.8762 (p0) cc_final: 0.8489 (p0) REVERT: B 403 ASP cc_start: 0.8510 (m-30) cc_final: 0.8259 (t0) REVERT: B 534 MET cc_start: 0.8659 (mmp) cc_final: 0.8372 (mmp) REVERT: B 608 ASP cc_start: 0.8937 (p0) cc_final: 0.8711 (p0) REVERT: B 741 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8215 (mm-30) REVERT: B 750 THR cc_start: 0.7972 (p) cc_final: 0.7552 (p) REVERT: B 786 VAL cc_start: 0.9264 (t) cc_final: 0.8984 (m) REVERT: B 1080 ARG cc_start: 0.7841 (ttp80) cc_final: 0.7264 (ttp80) REVERT: B 1096 SER cc_start: 0.9172 (p) cc_final: 0.8935 (p) REVERT: B 1105 MET cc_start: 0.8001 (mpp) cc_final: 0.7546 (mmt) REVERT: A 107 ARG cc_start: 0.9424 (mmm160) cc_final: 0.9122 (tmm160) REVERT: A 173 MET cc_start: 0.9739 (ttp) cc_final: 0.9459 (ppp) REVERT: A 241 CYS cc_start: 0.9039 (t) cc_final: 0.8640 (p) REVERT: A 456 ASP cc_start: 0.9250 (m-30) cc_final: 0.8761 (t0) REVERT: A 483 CYS cc_start: 0.8900 (m) cc_final: 0.7959 (t) REVERT: A 492 GLU cc_start: 0.9288 (mt-10) cc_final: 0.9003 (mp0) REVERT: A 494 MET cc_start: 0.9461 (mmt) cc_final: 0.8522 (mmt) REVERT: A 542 HIS cc_start: 0.9085 (m-70) cc_final: 0.8714 (p-80) REVERT: A 704 MET cc_start: 0.7746 (tpp) cc_final: 0.7270 (tpp) REVERT: A 720 TYR cc_start: 0.8391 (m-10) cc_final: 0.8147 (m-80) outliers start: 66 outliers final: 54 residues processed: 411 average time/residue: 0.1422 time to fit residues: 91.6283 Evaluate side-chains 397 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 341 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 557 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 45 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 254 optimal weight: 0.5980 chunk 136 optimal weight: 8.9990 chunk 187 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 144 optimal weight: 0.4980 chunk 8 optimal weight: 30.0000 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 357 HIS D 77 ASN ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.117232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.083277 restraints weight = 60656.678| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 5.79 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21240 Z= 0.147 Angle : 0.657 14.322 28717 Z= 0.327 Chirality : 0.044 0.290 3238 Planarity : 0.004 0.050 3679 Dihedral : 5.419 87.785 2849 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.02 % Allowed : 19.71 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -1.10 (0.16), residues: 2590 helix: 1.33 (0.20), residues: 733 sheet: -1.08 (0.20), residues: 642 loop : -1.84 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 15 TYR 0.016 0.001 TYR D 134 PHE 0.015 0.001 PHE B 799 TRP 0.013 0.001 TRP C 415 HIS 0.005 0.001 HIS I 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (21216) covalent geometry : angle 0.65143 / 0.33 (28699) SS BOND : bond 0.00015 / 0.01 ( 1) SS BOND : angle 0.06278 / 0.04 ( 2) hydrogen bonds : bond 0.03526 / 2.42 ( 798) hydrogen bonds : angle 4.56258 / 3.18 ( 2298) metal coordination : bond 0.00790 / 0.39 ( 23) metal coordination : angle 3.73503 / 2.52 ( 16) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 351 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8724 (mm) REVERT: C 198 GLN cc_start: 0.7691 (pp30) cc_final: 0.6847 (pp30) REVERT: C 228 GLN cc_start: 0.8440 (tt0) cc_final: 0.7996 (tm-30) REVERT: C 306 GLN cc_start: 0.9012 (mt0) cc_final: 0.8734 (mt0) REVERT: C 330 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7283 (mp0) REVERT: C 358 GLU cc_start: 0.8603 (mp0) cc_final: 0.8340 (mp0) REVERT: C 422 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9080 (mp) REVERT: D 34 GLN cc_start: 0.9021 (tt0) cc_final: 0.8545 (tp-100) REVERT: D 36 THR cc_start: 0.9422 (m) cc_final: 0.9146 (p) REVERT: D 55 HIS cc_start: 0.9018 (m170) cc_final: 0.8736 (m-70) REVERT: D 66 LYS cc_start: 0.9376 (ttmm) cc_final: 0.9049 (ttmm) REVERT: D 90 ARG cc_start: 0.8288 (ptp90) cc_final: 0.7939 (ptp-170) REVERT: D 125 GLN cc_start: 0.9561 (tp40) cc_final: 0.9182 (tp-100) REVERT: D 139 ARG cc_start: 0.8892 (mtm180) cc_final: 0.8379 (mmp80) REVERT: D 145 TYR cc_start: 0.8913 (m-80) cc_final: 0.8551 (m-80) REVERT: I 150 GLN cc_start: 0.8847 (tt0) cc_final: 0.8210 (tt0) REVERT: N 1 MET cc_start: 0.8548 (mtp) cc_final: 0.8206 (mtm) REVERT: N 4 LYS cc_start: 0.9083 (mtpt) cc_final: 0.8754 (mtpp) REVERT: N 44 ILE cc_start: 0.9078 (mt) cc_final: 0.8653 (mm) REVERT: N 54 LYS cc_start: 0.9220 (mmtp) cc_final: 0.8996 (mmmm) REVERT: U 34 GLU cc_start: 0.8665 (tp30) cc_final: 0.8010 (tm-30) REVERT: U 41 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7418 (mp10) REVERT: U 51 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7960 (pm20) REVERT: R 55 GLU cc_start: 0.9225 (tp30) cc_final: 0.8603 (tm-30) REVERT: R 100 GLU cc_start: 0.9146 (mp0) cc_final: 0.8755 (mm-30) REVERT: B 1 MET cc_start: 0.7980 (mmm) cc_final: 0.7599 (mmp) REVERT: B 130 MET cc_start: 0.8618 (ppp) cc_final: 0.8361 (ppp) REVERT: B 158 ARG cc_start: 0.8861 (mmm-85) cc_final: 0.8504 (mmm-85) REVERT: B 218 MET cc_start: 0.8714 (tpp) cc_final: 0.8262 (ttm) REVERT: B 275 ASP cc_start: 0.8676 (p0) cc_final: 0.8367 (p0) REVERT: B 277 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8506 (mm-30) REVERT: B 282 MET cc_start: 0.8838 (tpt) cc_final: 0.8612 (tpt) REVERT: B 312 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8542 (tm-30) REVERT: B 315 THR cc_start: 0.8111 (p) cc_final: 0.7746 (p) REVERT: B 366 ASP cc_start: 0.8844 (p0) cc_final: 0.8575 (p0) REVERT: B 403 ASP cc_start: 0.8551 (m-30) cc_final: 0.8284 (t0) REVERT: B 534 MET cc_start: 0.8679 (mmp) cc_final: 0.8397 (mmp) REVERT: B 581 MET cc_start: 0.9116 (mmt) cc_final: 0.8830 (mmp) REVERT: B 608 ASP cc_start: 0.8957 (p0) cc_final: 0.8748 (p0) REVERT: B 741 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8182 (mm-30) REVERT: B 750 THR cc_start: 0.8008 (p) cc_final: 0.7599 (p) REVERT: B 786 VAL cc_start: 0.9253 (t) cc_final: 0.8974 (m) REVERT: B 1080 ARG cc_start: 0.7860 (ttp80) cc_final: 0.7290 (ttp80) REVERT: B 1096 SER cc_start: 0.9182 (p) cc_final: 0.8928 (p) REVERT: B 1105 MET cc_start: 0.7991 (mpp) cc_final: 0.7555 (mmt) REVERT: A 107 ARG cc_start: 0.9414 (mmm160) cc_final: 0.9125 (tmm160) REVERT: A 173 MET cc_start: 0.9744 (ttp) cc_final: 0.9468 (ppp) REVERT: A 241 CYS cc_start: 0.9060 (t) cc_final: 0.8660 (p) REVERT: A 456 ASP cc_start: 0.9265 (m-30) cc_final: 0.8774 (t0) REVERT: A 483 CYS cc_start: 0.8889 (m) cc_final: 0.7969 (t) REVERT: A 492 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8993 (mp0) REVERT: A 494 MET cc_start: 0.9441 (mmt) cc_final: 0.8491 (mmt) REVERT: A 542 HIS cc_start: 0.9068 (m-70) cc_final: 0.8712 (p-80) REVERT: A 704 MET cc_start: 0.7836 (tpp) cc_final: 0.7513 (tpp) REVERT: A 720 TYR cc_start: 0.8432 (m-10) cc_final: 0.8178 (m-80) outliers start: 69 outliers final: 58 residues processed: 397 average time/residue: 0.1485 time to fit residues: 91.5582 Evaluate side-chains 406 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 345 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain U residue 41 GLN Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1014 MET Chi-restraints excluded: chain B residue 1027 SER Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 557 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 240 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 223 optimal weight: 0.7980 chunk 237 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 77 ASN ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 845 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.116722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.082497 restraints weight = 61433.234| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 5.87 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21240 Z= 0.177 Angle : 0.675 14.832 28717 Z= 0.337 Chirality : 0.044 0.265 3238 Planarity : 0.004 0.046 3679 Dihedral : 5.479 88.094 2849 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.85 % Allowed : 20.02 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.16), residues: 2590 helix: 1.30 (0.20), residues: 733 sheet: -1.10 (0.20), residues: 638 loop : -1.86 (0.16), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1080 TYR 0.014 0.001 TYR C 59 PHE 0.018 0.001 PHE B 799 TRP 0.014 0.001 TRP B1047 HIS 0.006 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (21216) covalent geometry : angle 0.66882 / 0.34 (28699) SS BOND : bond 0.00014 / 0.01 ( 1) SS BOND : angle 0.20217 / 0.11 ( 2) hydrogen bonds : bond 0.03687 / 2.53 ( 798) hydrogen bonds : angle 4.59927 / 3.20 ( 2298) metal coordination : bond 0.00951 / 0.46 ( 23) metal coordination : angle 4.01394 / 2.68 ( 16) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 349 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 59 TYR cc_start: 0.6783 (p90) cc_final: 0.6374 (p90) REVERT: C 185 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8706 (mm) REVERT: C 198 GLN cc_start: 0.7709 (pp30) cc_final: 0.6890 (pp30) REVERT: C 228 GLN cc_start: 0.8491 (tt0) cc_final: 0.7996 (tm-30) REVERT: C 262 ARG cc_start: 0.9080 (ttm-80) cc_final: 0.8703 (ttm-80) REVERT: C 306 GLN cc_start: 0.9022 (mt0) cc_final: 0.8732 (mt0) REVERT: C 330 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7297 (mp0) REVERT: C 422 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9079 (mp) REVERT: D 34 GLN cc_start: 0.9058 (tt0) cc_final: 0.8601 (tp-100) REVERT: D 36 THR cc_start: 0.9426 (m) cc_final: 0.9167 (p) REVERT: D 55 HIS cc_start: 0.9020 (m170) cc_final: 0.8742 (m-70) REVERT: D 66 LYS cc_start: 0.9383 (ttmm) cc_final: 0.9064 (ttmm) REVERT: D 90 ARG cc_start: 0.8208 (ptp90) cc_final: 0.7889 (ptp-170) REVERT: D 125 GLN cc_start: 0.9571 (tp40) cc_final: 0.9191 (tp-100) REVERT: D 139 ARG cc_start: 0.8910 (mtm180) cc_final: 0.8364 (mmp80) REVERT: D 145 TYR cc_start: 0.8937 (m-80) cc_final: 0.8526 (m-80) REVERT: I 150 GLN cc_start: 0.8897 (tt0) cc_final: 0.8369 (tt0) REVERT: N 1 MET cc_start: 0.8590 (mtp) cc_final: 0.8252 (mtm) REVERT: N 4 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8752 (mtpp) REVERT: N 44 ILE cc_start: 0.9055 (mt) cc_final: 0.8616 (mm) REVERT: N 54 LYS cc_start: 0.9190 (mmtp) cc_final: 0.8961 (mmmm) REVERT: U 34 GLU cc_start: 0.8697 (tp30) cc_final: 0.8035 (tm-30) REVERT: U 51 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8182 (pm20) REVERT: R 55 GLU cc_start: 0.9288 (tp30) cc_final: 0.8626 (tm-30) REVERT: R 92 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7069 (tm-30) REVERT: R 100 GLU cc_start: 0.9168 (mp0) cc_final: 0.8670 (mm-30) REVERT: B 1 MET cc_start: 0.8028 (mmm) cc_final: 0.7666 (mmp) REVERT: B 130 MET cc_start: 0.8665 (ppp) cc_final: 0.8383 (ppp) REVERT: B 158 ARG cc_start: 0.8877 (mmm-85) cc_final: 0.8521 (mmm-85) REVERT: B 218 MET cc_start: 0.8754 (tpp) cc_final: 0.8299 (ttp) REVERT: B 254 LYS cc_start: 0.9096 (mptt) cc_final: 0.8658 (mppt) REVERT: B 275 ASP cc_start: 0.8694 (p0) cc_final: 0.8391 (p0) REVERT: B 277 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8462 (mm-30) REVERT: B 282 MET cc_start: 0.8810 (tpt) cc_final: 0.8601 (tpt) REVERT: B 312 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8573 (tm-30) REVERT: B 315 THR cc_start: 0.8222 (p) cc_final: 0.7872 (p) REVERT: B 366 ASP cc_start: 0.8859 (p0) cc_final: 0.8588 (p0) REVERT: B 403 ASP cc_start: 0.8546 (m-30) cc_final: 0.8288 (t0) REVERT: B 534 MET cc_start: 0.8734 (mmp) cc_final: 0.8465 (mmp) REVERT: B 608 ASP cc_start: 0.8978 (p0) cc_final: 0.8773 (p0) REVERT: B 741 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8147 (mm-30) REVERT: B 750 THR cc_start: 0.7959 (p) cc_final: 0.7526 (p) REVERT: B 786 VAL cc_start: 0.9254 (t) cc_final: 0.8974 (m) REVERT: B 796 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8294 (pt0) REVERT: B 1080 ARG cc_start: 0.7848 (ttp80) cc_final: 0.7297 (ttp80) REVERT: B 1096 SER cc_start: 0.9223 (p) cc_final: 0.8974 (p) REVERT: B 1105 MET cc_start: 0.8048 (mpp) cc_final: 0.7716 (mmm) REVERT: A 107 ARG cc_start: 0.9411 (mmm160) cc_final: 0.9134 (tmm160) REVERT: A 173 MET cc_start: 0.9757 (ttp) cc_final: 0.9467 (ppp) REVERT: A 241 CYS cc_start: 0.9055 (t) cc_final: 0.8661 (p) REVERT: A 456 ASP cc_start: 0.9278 (m-30) cc_final: 0.8779 (t0) REVERT: A 483 CYS cc_start: 0.8909 (m) cc_final: 0.8269 (t) REVERT: A 492 GLU cc_start: 0.9297 (mt-10) cc_final: 0.9032 (mp0) REVERT: A 494 MET cc_start: 0.9401 (mmt) cc_final: 0.8691 (mmt) REVERT: A 542 HIS cc_start: 0.9115 (m-70) cc_final: 0.8739 (p-80) REVERT: A 704 MET cc_start: 0.7764 (tpp) cc_final: 0.7467 (tpp) REVERT: A 706 MET cc_start: 0.8882 (pmm) cc_final: 0.8678 (pmm) REVERT: A 720 TYR cc_start: 0.8420 (m-10) cc_final: 0.8185 (m-80) outliers start: 65 outliers final: 57 residues processed: 391 average time/residue: 0.1500 time to fit residues: 91.5612 Evaluate side-chains 398 residues out of total 2338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 339 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 300 LYS Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 313 ASP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 397 HIS Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 77 ASN Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 87 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 427 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 437 MET Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 643 SER Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 870 VAL Chi-restraints excluded: chain B residue 888 VAL Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 997 LEU Chi-restraints excluded: chain B residue 1004 VAL Chi-restraints excluded: chain B residue 1014 MET Chi-restraints excluded: chain B residue 1036 MET Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1058 LEU Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1120 MET Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 CYS Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 397 PHE Chi-restraints excluded: chain A residue 557 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 249 optimal weight: 50.0000 chunk 98 optimal weight: 0.8980 chunk 254 optimal weight: 0.0270 chunk 83 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 175 optimal weight: 8.9990 overall best weight: 1.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 77 ASN ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.117902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.084083 restraints weight = 60772.120| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 5.76 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21240 Z= 0.123 Angle : 0.673 16.144 28717 Z= 0.332 Chirality : 0.044 0.273 3238 Planarity : 0.004 0.051 3679 Dihedral : 5.325 86.364 2849 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.50 % Allowed : 20.32 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.16), residues: 2590 helix: 1.42 (0.20), residues: 727 sheet: -1.01 (0.20), residues: 639 loop : -1.82 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1080 TYR 0.033 0.001 TYR I 181 PHE 0.015 0.001 PHE B 949 TRP 0.018 0.001 TRP B 893 HIS 0.004 0.001 HIS I 196 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 (21216) covalent geometry : angle 0.66776 / 0.33 (28699) SS BOND : bond 0.00056 / 0.03 ( 1) SS BOND : angle 0.44763 / 0.24 ( 2) hydrogen bonds : bond 0.03393 / 2.33 ( 798) hydrogen bonds : angle 4.48951 / 3.12 ( 2298) metal coordination : bond 0.00640 / 0.33 ( 23) metal coordination : angle 3.46444 / 2.30 ( 16) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5066.13 seconds wall clock time: 87 minutes 41.28 seconds (5261.28 seconds total)