Starting phenix.real_space_refine on Sat Feb 7 13:36:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2u_38020/02_2026/8x2u_38020.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2u_38020/02_2026/8x2u_38020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x2u_38020/02_2026/8x2u_38020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2u_38020/02_2026/8x2u_38020.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2u_38020/02_2026/8x2u_38020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2u_38020/02_2026/8x2u_38020.cif" } resolution = 3.57 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= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 21708 2.51 5 N 5746 2.21 5 O 6340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 220 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33922 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 369 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "B" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1489 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 16, 'TRANS': 161} Chain: "D" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 387 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 17, 'TRANS': 183} Chain: "F" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1514 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 4, 'TRANS': 180} Chain: "G" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3099 Classifications: {'peptide': 387} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 30, 'TRANS': 352} Chain breaks: 5 Chain: "H" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1912 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 226} Chain breaks: 2 Chain: "I" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1514 Classifications: {'peptide': 185} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 178} Chain: "J" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3139 Classifications: {'peptide': 392} Link IDs: {'CIS': 3, 'PTRANS': 31, 'TRANS': 357} Chain breaks: 5 Chain: "c" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1926 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 228} Chain breaks: 2 Chain: "C" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 369 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "K" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1489 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 16, 'TRANS': 162} Chain: "L" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 387 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "M" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 17, 'TRANS': 183} Chain: "N" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1514 Classifications: {'peptide': 185} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 179} Chain: "O" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3099 Classifications: {'peptide': 387} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 30, 'TRANS': 353} Chain breaks: 5 Chain: "P" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1912 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 225} Chain breaks: 2 Chain: "Q" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1514 Classifications: {'peptide': 185} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 178} Chain: "R" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3139 Classifications: {'peptide': 392} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 30, 'TRANS': 358} Chain breaks: 5 Chain: "d" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1926 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 225} Chain breaks: 2 Time building chain proxies: 7.75, per 1000 atoms: 0.23 Number of scatterers: 33922 At special positions: 0 Unit cell: (252.784, 181.902, 132.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 6340 8.00 N 5746 7.00 C 21708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.71 Conformation dependent library (CDL) restraints added in 1.2 seconds 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7764 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 50 sheets defined 31.7% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 4.157A pdb=" N LEU A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 11 " --> pdb=" O LYS A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 28 through 45 Processing helix chain 'B' and resid 148 through 154 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 303 through 315 Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.619A pdb=" N GLY D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 330 removed outlier: 3.535A pdb=" N GLU D 329 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 38 removed outlier: 3.504A pdb=" N GLY E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 58 Processing helix chain 'E' and resid 67 through 76 removed outlier: 3.645A pdb=" N THR E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER E 75 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 98 Processing helix chain 'E' and resid 101 through 109 removed outlier: 3.650A pdb=" N GLU E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 118 Processing helix chain 'E' and resid 131 through 143 removed outlier: 3.739A pdb=" N PHE E 143 " --> pdb=" O ILE E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 164 Processing helix chain 'E' and resid 165 through 180 removed outlier: 4.005A pdb=" N GLN E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 195 removed outlier: 4.548A pdb=" N TRP E 187 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 219 removed outlier: 3.749A pdb=" N SER G 219 " --> pdb=" O ALA G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 242 Processing helix chain 'G' and resid 246 through 249 removed outlier: 3.857A pdb=" N ASP G 249 " --> pdb=" O ASP G 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 246 through 249' Processing helix chain 'G' and resid 250 through 260 removed outlier: 3.741A pdb=" N GLN G 256 " --> pdb=" O GLU G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 275 No H-bonds generated for 'chain 'G' and resid 273 through 275' Processing helix chain 'G' and resid 276 through 291 removed outlier: 4.551A pdb=" N ALA G 288 " --> pdb=" O GLU G 284 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU G 289 " --> pdb=" O THR G 285 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE G 290 " --> pdb=" O GLN G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 325 Processing helix chain 'G' and resid 328 through 347 removed outlier: 4.234A pdb=" N GLU G 332 " --> pdb=" O LEU G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 423 through 427 Processing helix chain 'G' and resid 447 through 452 Processing helix chain 'G' and resid 453 through 457 removed outlier: 3.925A pdb=" N LYS G 456 " --> pdb=" O THR G 453 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 495 removed outlier: 4.310A pdb=" N GLY G 493 " --> pdb=" O ARG G 489 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS G 495 " --> pdb=" O SER G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 533 through 538 removed outlier: 3.760A pdb=" N SER G 538 " --> pdb=" O ASP G 534 " (cutoff:3.500A) Processing helix chain 'G' and resid 595 through 600 removed outlier: 3.757A pdb=" N ASP G 599 " --> pdb=" O ILE G 596 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU G 600 " --> pdb=" O SER G 597 " (cutoff:3.500A) Processing helix chain 'G' and resid 673 through 677 removed outlier: 3.656A pdb=" N THR G 677 " --> pdb=" O PRO G 674 " (cutoff:3.500A) Processing helix chain 'G' and resid 683 through 692 removed outlier: 3.554A pdb=" N MET G 692 " --> pdb=" O GLN G 688 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 9 Processing helix chain 'H' and resid 9 through 14 Processing helix chain 'H' and resid 21 through 39 Processing helix chain 'H' and resid 89 through 96 removed outlier: 4.007A pdb=" N ILE H 96 " --> pdb=" O MET H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 99 No H-bonds generated for 'chain 'H' and resid 97 through 99' Processing helix chain 'H' and resid 136 through 151 Processing helix chain 'H' and resid 177 through 182 removed outlier: 4.220A pdb=" N ARG H 182 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'H' and resid 271 through 276 removed outlier: 3.649A pdb=" N MET H 275 " --> pdb=" O ASP H 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 218 Processing helix chain 'J' and resid 227 through 242 Processing helix chain 'J' and resid 249 through 261 removed outlier: 4.502A pdb=" N ASN J 253 " --> pdb=" O ASP J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 287 removed outlier: 3.979A pdb=" N GLU J 281 " --> pdb=" O LEU J 277 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 325 Processing helix chain 'J' and resid 328 through 347 removed outlier: 4.241A pdb=" N GLU J 332 " --> pdb=" O LEU J 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 447 through 452 Processing helix chain 'J' and resid 453 through 457 removed outlier: 4.007A pdb=" N LYS J 456 " --> pdb=" O THR J 453 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE J 457 " --> pdb=" O ALA J 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 453 through 457' Processing helix chain 'J' and resid 478 through 495 Processing helix chain 'J' and resid 531 through 538 removed outlier: 3.572A pdb=" N VAL J 536 " --> pdb=" O VAL J 532 " (cutoff:3.500A) Processing helix chain 'J' and resid 595 through 599 removed outlier: 3.663A pdb=" N GLU J 598 " --> pdb=" O PRO J 595 " (cutoff:3.500A) Processing helix chain 'J' and resid 673 through 678 Processing helix chain 'J' and resid 683 through 693 Processing helix chain 'c' and resid 2 through 6 removed outlier: 4.181A pdb=" N LEU c 6 " --> pdb=" O ALA c 3 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 15 Processing helix chain 'c' and resid 21 through 39 Processing helix chain 'c' and resid 89 through 96 Processing helix chain 'c' and resid 97 through 99 No H-bonds generated for 'chain 'c' and resid 97 through 99' Processing helix chain 'c' and resid 135 through 149 Processing helix chain 'c' and resid 177 through 182 removed outlier: 4.050A pdb=" N ARG c 182 " --> pdb=" O LEU c 178 " (cutoff:3.500A) Processing helix chain 'c' and resid 271 through 275 Processing helix chain 'C' and resid 2 through 10 removed outlier: 3.638A pdb=" N LEU C 6 " --> pdb=" O ASP C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 25 removed outlier: 4.060A pdb=" N THR C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 45 Processing helix chain 'K' and resid 147 through 154 Processing helix chain 'K' and resid 303 through 315 removed outlier: 3.545A pdb=" N LEU K 315 " --> pdb=" O ARG K 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 291 removed outlier: 3.555A pdb=" N GLY L 290 " --> pdb=" O ASP L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 291 through 330 removed outlier: 3.617A pdb=" N HIS L 330 " --> pdb=" O ASN L 326 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 25 No H-bonds generated for 'chain 'M' and resid 23 through 25' Processing helix chain 'M' and resid 26 through 38 removed outlier: 3.610A pdb=" N GLY M 38 " --> pdb=" O ILE M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 58 Processing helix chain 'M' and resid 67 through 76 removed outlier: 3.603A pdb=" N MET M 74 " --> pdb=" O LEU M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 98 Processing helix chain 'M' and resid 101 through 109 removed outlier: 4.467A pdb=" N GLU M 107 " --> pdb=" O LEU M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 118 Processing helix chain 'M' and resid 131 through 143 Processing helix chain 'M' and resid 154 through 165 removed outlier: 3.962A pdb=" N LYS M 158 " --> pdb=" O GLY M 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 180 removed outlier: 4.424A pdb=" N GLN M 171 " --> pdb=" O PRO M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 195 removed outlier: 4.411A pdb=" N TRP M 187 " --> pdb=" O ASP M 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 207 through 217 Processing helix chain 'O' and resid 227 through 240 Processing helix chain 'O' and resid 244 through 249 removed outlier: 4.535A pdb=" N VAL O 248 " --> pdb=" O ALA O 245 " (cutoff:3.500A) Processing helix chain 'O' and resid 250 through 261 removed outlier: 3.881A pdb=" N GLN O 256 " --> pdb=" O GLU O 252 " (cutoff:3.500A) Processing helix chain 'O' and resid 273 through 275 No H-bonds generated for 'chain 'O' and resid 273 through 275' Processing helix chain 'O' and resid 276 through 286 removed outlier: 3.726A pdb=" N TYR O 280 " --> pdb=" O MET O 276 " (cutoff:3.500A) Processing helix chain 'O' and resid 287 through 291 removed outlier: 3.814A pdb=" N LEU O 291 " --> pdb=" O ALA O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 313 through 323 Processing helix chain 'O' and resid 329 through 347 Processing helix chain 'O' and resid 423 through 428 removed outlier: 3.622A pdb=" N ASN O 426 " --> pdb=" O THR O 423 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N TYR O 428 " --> pdb=" O ALA O 425 " (cutoff:3.500A) Processing helix chain 'O' and resid 478 through 495 Processing helix chain 'O' and resid 531 through 538 removed outlier: 3.754A pdb=" N SER O 538 " --> pdb=" O ASP O 534 " (cutoff:3.500A) Processing helix chain 'O' and resid 595 through 599 removed outlier: 3.543A pdb=" N GLU O 598 " --> pdb=" O PRO O 595 " (cutoff:3.500A) Processing helix chain 'O' and resid 617 through 621 Processing helix chain 'O' and resid 673 through 677 removed outlier: 3.665A pdb=" N ILE O 676 " --> pdb=" O GLY O 673 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR O 677 " --> pdb=" O PRO O 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 673 through 677' Processing helix chain 'O' and resid 683 through 692 Processing helix chain 'P' and resid 3 through 8 removed outlier: 3.706A pdb=" N LEU P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 14 Processing helix chain 'P' and resid 21 through 39 Processing helix chain 'P' and resid 89 through 96 removed outlier: 3.763A pdb=" N ILE P 96 " --> pdb=" O MET P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 99 No H-bonds generated for 'chain 'P' and resid 97 through 99' Processing helix chain 'P' and resid 136 through 152 removed outlier: 3.596A pdb=" N ALA P 152 " --> pdb=" O ASP P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 182 removed outlier: 4.107A pdb=" N ARG P 182 " --> pdb=" O LEU P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 185 No H-bonds generated for 'chain 'P' and resid 183 through 185' Processing helix chain 'P' and resid 216 through 220 removed outlier: 4.005A pdb=" N TYR P 219 " --> pdb=" O SER P 216 " (cutoff:3.500A) Processing helix chain 'P' and resid 232 through 235 Processing helix chain 'P' and resid 271 through 276 Processing helix chain 'Q' and resid 71 through 75 removed outlier: 3.598A pdb=" N ASN Q 74 " --> pdb=" O TYR Q 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 218 Processing helix chain 'R' and resid 227 through 243 Processing helix chain 'R' and resid 249 through 261 removed outlier: 4.631A pdb=" N ASN R 253 " --> pdb=" O ASP R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 287 removed outlier: 4.041A pdb=" N ILE R 282 " --> pdb=" O PRO R 278 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 291 Processing helix chain 'R' and resid 313 through 323 Processing helix chain 'R' and resid 328 through 347 removed outlier: 4.245A pdb=" N GLU R 332 " --> pdb=" O LEU R 328 " (cutoff:3.500A) Processing helix chain 'R' and resid 424 through 428 removed outlier: 4.571A pdb=" N TYR R 428 " --> pdb=" O ALA R 425 " (cutoff:3.500A) Processing helix chain 'R' and resid 447 through 451 Processing helix chain 'R' and resid 478 through 495 Processing helix chain 'R' and resid 531 through 538 Processing helix chain 'R' and resid 595 through 599 Processing helix chain 'R' and resid 683 through 693 Processing helix chain 'd' and resid 11 through 15 Processing helix chain 'd' and resid 21 through 39 removed outlier: 3.857A pdb=" N ARG d 37 " --> pdb=" O MET d 33 " (cutoff:3.500A) Processing helix chain 'd' and resid 89 through 97 Processing helix chain 'd' and resid 136 through 149 Processing helix chain 'd' and resid 177 through 182 removed outlier: 3.657A pdb=" N ARG d 182 " --> pdb=" O LEU d 178 " (cutoff:3.500A) Processing helix chain 'd' and resid 183 through 185 No H-bonds generated for 'chain 'd' and resid 183 through 185' Processing helix chain 'd' and resid 271 through 276 removed outlier: 3.772A pdb=" N MET d 275 " --> pdb=" O ASP d 271 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 142 through 147 removed outlier: 6.227A pdb=" N ARG B 142 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 214 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 218 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 155 through 160 Processing sheet with id=AA3, first strand: chain 'B' and resid 193 through 195 removed outlier: 3.709A pdb=" N THR B 195 " --> pdb=" O LYS E 201 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 223 through 226 removed outlier: 3.516A pdb=" N ASN B 229 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 230 " --> pdb=" O ASP B 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 245 through 250 Processing sheet with id=AA6, first strand: chain 'E' and resid 14 through 19 removed outlier: 4.133A pdb=" N GLN E 43 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ALA E 85 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE E 41 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 19 through 21 removed outlier: 3.555A pdb=" N ALA F 36 " --> pdb=" O TYR F 44 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ARG F 66 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR F 81 " --> pdb=" O ARG F 66 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR F 68 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLN F 79 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASP F 70 " --> pdb=" O HIS F 77 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS F 77 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN F 125 " --> pdb=" O GLU F 116 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE F 118 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N HIS F 123 " --> pdb=" O PHE F 118 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA F 149 " --> pdb=" O THR F 140 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS F 162 " --> pdb=" O PRO F 171 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU F 188 " --> pdb=" O PRO F 168 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS F 180 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU F 181 " --> pdb=" O GLU F 197 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLU F 197 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N HIS F 183 " --> pdb=" O GLU F 195 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU F 195 " --> pdb=" O HIS F 183 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU F 185 " --> pdb=" O ARG F 193 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG F 187 " --> pdb=" O THR F 191 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N THR F 191 " --> pdb=" O ARG F 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 94 through 95 Processing sheet with id=AA9, first strand: chain 'G' and resid 441 through 442 removed outlier: 3.600A pdb=" N CYS G 433 " --> pdb=" O ILE G 366 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL G 367 " --> pdb=" O TRP G 355 " (cutoff:3.500A) removed outlier: 19.916A pdb=" N PHE G 642 " --> pdb=" O ILE G 349 " (cutoff:3.500A) removed outlier: 14.667A pdb=" N ARG G 351 " --> pdb=" O PHE G 642 " (cutoff:3.500A) removed outlier: 13.627A pdb=" N ASN G 644 " --> pdb=" O ARG G 351 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ARG G 353 " --> pdb=" O ASN G 644 " (cutoff:3.500A) removed outlier: 9.422A pdb=" N TYR G 646 " --> pdb=" O ARG G 353 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TRP G 355 " --> pdb=" O TYR G 646 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLY G 648 " --> pdb=" O TRP G 355 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LYS G 357 " --> pdb=" O GLY G 648 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER G 637 " --> pdb=" O ALA G 623 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 496 through 498 Processing sheet with id=AB2, first strand: chain 'G' and resid 502 through 503 Processing sheet with id=AB3, first strand: chain 'H' and resid 83 through 84 removed outlier: 6.665A pdb=" N TYR H 57 " --> pdb=" O ARG H 49 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ARG H 49 " --> pdb=" O TYR H 57 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE H 59 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 9.457A pdb=" N TYR H 262 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP H 47 " --> pdb=" O TYR H 262 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLY H 264 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ARG H 49 " --> pdb=" O GLY H 264 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 110 through 111 Processing sheet with id=AB5, first strand: chain 'H' and resid 153 through 155 Processing sheet with id=AB6, first strand: chain 'H' and resid 160 through 162 removed outlier: 3.854A pdb=" N VAL H 166 " --> pdb=" O THR H 162 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 226 through 230 removed outlier: 3.830A pdb=" N GLY H 259 " --> pdb=" O TYR H 250 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 23 through 24 removed outlier: 4.004A pdb=" N GLU I 23 " --> pdb=" O HIS I 31 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N HIS I 31 " --> pdb=" O GLU I 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 34 through 37 removed outlier: 3.567A pdb=" N GLY I 78 " --> pdb=" O TRP I 94 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY I 80 " --> pdb=" O GLY I 92 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY I 92 " --> pdb=" O GLY I 80 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN I 102 " --> pdb=" O GLU I 93 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLY I 101 " --> pdb=" O TRP I 117 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR I 112 " --> pdb=" O LEU I 129 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLN I 125 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR I 140 " --> pdb=" O ALA I 149 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA I 149 " --> pdb=" O THR I 140 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL I 142 " --> pdb=" O GLU I 147 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU I 147 " --> pdb=" O VAL I 142 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY I 148 " --> pdb=" O PHE I 163 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N PHE I 163 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS I 162 " --> pdb=" O PRO I 171 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N MET I 164 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL I 169 " --> pdb=" O MET I 164 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N HIS I 183 " --> pdb=" O GLU I 195 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 48 through 49 Processing sheet with id=AC2, first strand: chain 'J' and resid 441 through 442 removed outlier: 6.945A pdb=" N VAL J 367 " --> pdb=" O TRP J 355 " (cutoff:3.500A) removed outlier: 19.667A pdb=" N PHE J 642 " --> pdb=" O ILE J 349 " (cutoff:3.500A) removed outlier: 14.469A pdb=" N ARG J 351 " --> pdb=" O PHE J 642 " (cutoff:3.500A) removed outlier: 14.339A pdb=" N ASN J 644 " --> pdb=" O ARG J 351 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N ARG J 353 " --> pdb=" O ASN J 644 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N TYR J 646 " --> pdb=" O ARG J 353 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP J 355 " --> pdb=" O TYR J 646 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N GLY J 648 " --> pdb=" O TRP J 355 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LYS J 357 " --> pdb=" O GLY J 648 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ALA J 633 " --> pdb=" O SER J 627 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 496 through 498 Processing sheet with id=AC4, first strand: chain 'J' and resid 502 through 503 Processing sheet with id=AC5, first strand: chain 'c' and resid 83 through 84 removed outlier: 6.547A pdb=" N TYR c 57 " --> pdb=" O ARG c 49 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ARG c 49 " --> pdb=" O TYR c 57 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE c 59 " --> pdb=" O TRP c 47 " (cutoff:3.500A) removed outlier: 14.929A pdb=" N TYR c 258 " --> pdb=" O ARG c 43 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N LEU c 45 " --> pdb=" O TYR c 258 " (cutoff:3.500A) removed outlier: 9.382A pdb=" N TYR c 260 " --> pdb=" O LEU c 45 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N TRP c 47 " --> pdb=" O TYR c 260 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY c 264 " --> pdb=" O ARG c 49 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU c 247 " --> pdb=" O SER c 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS c 251 " --> pdb=" O VAL c 237 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 153 through 155 Processing sheet with id=AC7, first strand: chain 'K' and resid 143 through 146 removed outlier: 3.623A pdb=" N LEU K 144 " --> pdb=" O ILE K 214 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS K 216 " --> pdb=" O LEU K 144 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 156 through 160 Processing sheet with id=AC9, first strand: chain 'K' and resid 209 through 210 Processing sheet with id=AD1, first strand: chain 'K' and resid 224 through 225 removed outlier: 6.147A pdb=" N LEU K 230 " --> pdb=" O PHE K 291 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE K 293 " --> pdb=" O LEU K 230 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N PHE K 232 " --> pdb=" O PHE K 293 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 245 through 250 Processing sheet with id=AD3, first strand: chain 'M' and resid 40 through 47 removed outlier: 6.875A pdb=" N ILE M 83 " --> pdb=" O ILE M 42 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG M 44 " --> pdb=" O ALA M 81 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA M 81 " --> pdb=" O ARG M 44 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LYS M 46 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU M 79 " --> pdb=" O LYS M 46 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS M 127 " --> pdb=" O LEU M 18 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 19 through 21 removed outlier: 3.805A pdb=" N TYR N 67 " --> pdb=" O TYR N 59 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN N 79 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLN N 102 " --> pdb=" O GLU N 93 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA N 95 " --> pdb=" O HIS N 100 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N HIS N 100 " --> pdb=" O ALA N 95 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLN N 125 " --> pdb=" O GLU N 116 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N PHE N 118 " --> pdb=" O HIS N 123 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS N 123 " --> pdb=" O PHE N 118 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN N 160 " --> pdb=" O PRO N 171 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS N 162 " --> pdb=" O VAL N 169 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 19 through 21 removed outlier: 3.805A pdb=" N TYR N 67 " --> pdb=" O TYR N 59 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN N 79 " --> pdb=" O ASP N 70 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLN N 102 " --> pdb=" O GLU N 93 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA N 95 " --> pdb=" O HIS N 100 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N HIS N 100 " --> pdb=" O ALA N 95 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLN N 125 " --> pdb=" O GLU N 116 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N PHE N 118 " --> pdb=" O HIS N 123 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS N 123 " --> pdb=" O PHE N 118 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS N 180 " --> pdb=" O PHE N 176 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU N 199 " --> pdb=" O GLU N 181 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 349 through 358 removed outlier: 6.989A pdb=" N VAL O 367 " --> pdb=" O TRP O 355 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS O 357 " --> pdb=" O TYR O 365 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N TYR O 365 " --> pdb=" O LYS O 357 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'O' and resid 496 through 498 Processing sheet with id=AD8, first strand: chain 'O' and resid 502 through 503 removed outlier: 4.020A pdb=" N GLU O 522 " --> pdb=" O GLN O 503 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 609 through 612 Processing sheet with id=AE1, first strand: chain 'P' and resid 83 through 84 removed outlier: 3.529A pdb=" N LYS P 72 " --> pdb=" O GLY P 62 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN P 61 " --> pdb=" O PHE P 46 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE P 46 " --> pdb=" O GLN P 61 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU P 63 " --> pdb=" O VAL P 44 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL P 44 " --> pdb=" O LEU P 63 " (cutoff:3.500A) removed outlier: 13.154A pdb=" N ARG P 43 " --> pdb=" O TYR P 258 " (cutoff:3.500A) removed outlier: 13.090A pdb=" N TYR P 260 " --> pdb=" O ARG P 43 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N LEU P 45 " --> pdb=" O TYR P 260 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N TYR P 262 " --> pdb=" O LEU P 45 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N TRP P 47 " --> pdb=" O TYR P 262 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLY P 264 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG P 49 " --> pdb=" O GLY P 264 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE P 261 " --> pdb=" O THR P 248 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU P 247 " --> pdb=" O SER P 241 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 110 through 111 Processing sheet with id=AE3, first strand: chain 'P' and resid 153 through 155 Processing sheet with id=AE4, first strand: chain 'P' and resid 159 through 162 removed outlier: 3.895A pdb=" N VAL P 166 " --> pdb=" O THR P 162 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 19 through 20 removed outlier: 6.621A pdb=" N SER Q 47 " --> pdb=" O GLN Q 56 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N GLN Q 56 " --> pdb=" O SER Q 47 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU Q 49 " --> pdb=" O HIS Q 54 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N HIS Q 54 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLN Q 125 " --> pdb=" O GLU Q 116 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE Q 118 " --> pdb=" O HIS Q 123 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N HIS Q 123 " --> pdb=" O PHE Q 118 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA Q 150 " --> pdb=" O GLY Q 161 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY Q 161 " --> pdb=" O ALA Q 150 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 145 through 146 removed outlier: 3.805A pdb=" N ALA Q 150 " --> pdb=" O GLY Q 161 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY Q 161 " --> pdb=" O ALA Q 150 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN Q 160 " --> pdb=" O LYS Q 173 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'R' and resid 349 through 356 removed outlier: 6.778A pdb=" N GLU R 371 " --> pdb=" O GLN R 350 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N CYS R 352 " --> pdb=" O GLU R 369 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU R 369 " --> pdb=" O CYS R 352 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE R 354 " --> pdb=" O VAL R 367 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL R 367 " --> pdb=" O PHE R 354 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 496 through 498 Processing sheet with id=AE9, first strand: chain 'R' and resid 502 through 503 Processing sheet with id=AF1, first strand: chain 'R' and resid 608 through 612 Processing sheet with id=AF2, first strand: chain 'd' and resid 83 through 85 removed outlier: 4.273A pdb=" N THR d 73 " --> pdb=" O LEU d 85 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY d 62 " --> pdb=" O LYS d 72 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR d 57 " --> pdb=" O ARG d 49 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG d 49 " --> pdb=" O TYR d 57 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE d 59 " --> pdb=" O TRP d 47 " (cutoff:3.500A) removed outlier: 10.434A pdb=" N LEU d 45 " --> pdb=" O TYR d 258 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N TYR d 260 " --> pdb=" O LEU d 45 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TRP d 47 " --> pdb=" O TYR d 260 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU d 247 " --> pdb=" O SER d 241 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU d 236 " --> pdb=" O GLU d 231 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU d 231 " --> pdb=" O LEU d 236 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'd' and resid 110 through 111 removed outlier: 3.817A pdb=" N ILE d 134 " --> pdb=" O TYR d 111 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'd' and resid 153 through 155 Processing sheet with id=AF5, first strand: chain 'd' and resid 159 through 161 1387 hydrogen bonds defined for protein. 3786 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: 7.52 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5956 1.32 - 1.45: 9635 1.45 - 1.58: 18981 1.58 - 1.70: 16 1.70 - 1.83: 218 Bond restraints: 34806 Sorted by residual: bond pdb=" CB ARG C 41 " pdb=" CG ARG C 41 " ideal model delta sigma weight residual 1.520 1.433 0.087 3.00e-02 1.11e+03 8.48e+00 bond pdb=" C ASN E 196 " pdb=" N PRO E 197 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.59e+00 bond pdb=" CA LEU O 240 " pdb=" C LEU O 240 " ideal model delta sigma weight residual 1.523 1.572 -0.049 1.80e-02 3.09e+03 7.45e+00 bond pdb=" CB MET K 309 " pdb=" CG MET K 309 " ideal model delta sigma weight residual 1.520 1.596 -0.076 3.00e-02 1.11e+03 6.47e+00 bond pdb=" C ALA P 252 " pdb=" N PRO P 253 " ideal model delta sigma weight residual 1.335 1.367 -0.032 1.28e-02 6.10e+03 6.40e+00 ... (remaining 34801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.29: 46798 5.29 - 10.59: 343 10.59 - 15.88: 33 15.88 - 21.17: 3 21.17 - 26.46: 3 Bond angle restraints: 47180 Sorted by residual: angle pdb=" C ALA R 245 " pdb=" N ASP R 246 " pdb=" CA ASP R 246 " ideal model delta sigma weight residual 121.70 148.16 -26.46 1.80e+00 3.09e-01 2.16e+02 angle pdb=" C GLU P 65 " pdb=" N ASP P 66 " pdb=" CA ASP P 66 " ideal model delta sigma weight residual 121.70 143.05 -21.35 1.80e+00 3.09e-01 1.41e+02 angle pdb=" C LEU J 616 " pdb=" N ILE J 617 " pdb=" CA ILE J 617 " ideal model delta sigma weight residual 121.70 141.50 -19.80 1.80e+00 3.09e-01 1.21e+02 angle pdb=" C TYR Q 159 " pdb=" N GLN Q 160 " pdb=" CA GLN Q 160 " ideal model delta sigma weight residual 121.70 140.12 -18.42 1.80e+00 3.09e-01 1.05e+02 angle pdb=" C ARG Q 99 " pdb=" N HIS Q 100 " pdb=" CA HIS Q 100 " ideal model delta sigma weight residual 121.70 137.54 -15.84 1.80e+00 3.09e-01 7.75e+01 ... (remaining 47175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18244 17.98 - 35.95: 1899 35.95 - 53.93: 418 53.93 - 71.91: 84 71.91 - 89.88: 43 Dihedral angle restraints: 20688 sinusoidal: 8526 harmonic: 12162 Sorted by residual: dihedral pdb=" CA LYS B 216 " pdb=" C LYS B 216 " pdb=" N GLU B 217 " pdb=" CA GLU B 217 " ideal model delta harmonic sigma weight residual 0.00 -43.42 43.42 0 5.00e+00 4.00e-02 7.54e+01 dihedral pdb=" CA SER G 613 " pdb=" C SER G 613 " pdb=" N SER G 614 " pdb=" CA SER G 614 " ideal model delta harmonic sigma weight residual 0.00 -39.36 39.36 0 5.00e+00 4.00e-02 6.20e+01 dihedral pdb=" CA ASP E 183 " pdb=" C ASP E 183 " pdb=" N PRO E 184 " pdb=" CA PRO E 184 " ideal model delta harmonic sigma weight residual -180.00 -143.96 -36.04 0 5.00e+00 4.00e-02 5.20e+01 ... (remaining 20685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4541 0.099 - 0.199: 408 0.199 - 0.298: 13 0.298 - 0.398: 1 0.398 - 0.497: 1 Chirality restraints: 4964 Sorted by residual: chirality pdb=" CG LEU L 295 " pdb=" CB LEU L 295 " pdb=" CD1 LEU L 295 " pdb=" CD2 LEU L 295 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CA TRP D 294 " pdb=" N TRP D 294 " pdb=" C TRP D 294 " pdb=" CB TRP D 294 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE c 147 " pdb=" CA ILE c 147 " pdb=" CG1 ILE c 147 " pdb=" CG2 ILE c 147 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 4961 not shown) Planarity restraints: 6150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 294 " -0.041 2.00e-02 2.50e+03 4.07e-02 4.14e+01 pdb=" CG TRP D 294 " 0.106 2.00e-02 2.50e+03 pdb=" CD1 TRP D 294 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TRP D 294 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP D 294 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP D 294 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP D 294 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 294 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 294 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP D 294 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU M 7 " -0.064 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO M 8 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO M 8 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO M 8 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 294 " 0.030 2.00e-02 2.50e+03 2.42e-02 1.46e+01 pdb=" CG TRP L 294 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP L 294 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP L 294 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP L 294 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP L 294 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP L 294 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 294 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 294 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP L 294 " 0.003 2.00e-02 2.50e+03 ... (remaining 6147 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 378 2.61 - 3.18: 28751 3.18 - 3.75: 53611 3.75 - 4.33: 74191 4.33 - 4.90: 122833 Nonbonded interactions: 279764 Sorted by model distance: nonbonded pdb=" O TYR J 216 " pdb=" OG SER J 219 " model vdw 2.037 3.040 nonbonded pdb=" OH TYR G 216 " pdb=" O PRO J 244 " model vdw 2.045 3.040 nonbonded pdb=" OG SER B 147 " pdb=" OD2 ASP B 150 " model vdw 2.068 3.040 nonbonded pdb=" OD1 ASN O 426 " pdb=" OG SER O 445 " model vdw 2.075 3.040 nonbonded pdb=" OG SER K 147 " pdb=" OD1 ASP K 150 " model vdw 2.079 3.040 ... (remaining 279759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'N' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = (chain 'J' and (resid 206 through 261 or resid 273 through 377 or resid 413 thro \ ugh 693)) selection = chain 'O' selection = (chain 'R' and (resid 206 through 261 or resid 273 through 377 or resid 413 thro \ ugh 693)) } ncs_group { reference = chain 'H' selection = chain 'P' selection = (chain 'c' and (resid 1 through 113 or resid 133 through 276)) selection = (chain 'd' and (resid 1 through 113 or resid 133 through 276)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 31.610 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 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 : 0.007 0.126 34806 Z= 0.306 Angle : 1.218 26.465 47180 Z= 0.647 Chirality : 0.055 0.497 4964 Planarity : 0.009 0.144 6150 Dihedral : 15.704 89.882 12924 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.67 % Favored : 94.14 % Rotamer: Outliers : 0.33 % Allowed : 20.31 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.51 % Twisted Proline : 0.39 % Twisted General : 0.13 % 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: -1.41 (0.12), residues: 4110 helix: -0.51 (0.14), residues: 1068 sheet: -1.16 (0.18), residues: 722 loop : -1.01 (0.12), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG c 37 TYR 0.056 0.003 TYR R 216 PHE 0.052 0.003 PHE F 61 TRP 0.106 0.002 TRP D 294 HIS 0.028 0.002 HIS Q 157 Details of bonding type rmsd covalent geometry : bond 0.00703 (34806) covalent geometry : angle 1.21766 (47180) hydrogen bonds : bond 0.20487 ( 1325) hydrogen bonds : angle 8.44351 ( 3786) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1201 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1189 time to evaluate : 1.338 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: D 294 TRP cc_start: 0.7906 (t60) cc_final: 0.7331 (t60) REVERT: D 298 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7492 (mm-30) REVERT: D 322 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7396 (mp0) REVERT: D 323 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7918 (ttm-80) REVERT: E 90 ILE cc_start: 0.8713 (mp) cc_final: 0.8044 (mm) REVERT: E 195 ASN cc_start: 0.7619 (m-40) cc_final: 0.7232 (m-40) REVERT: F 122 ARG cc_start: 0.7981 (mpp80) cc_final: 0.7700 (mtm-85) REVERT: F 142 VAL cc_start: 0.8878 (t) cc_final: 0.8513 (m) REVERT: G 251 ILE cc_start: 0.8366 (tt) cc_final: 0.8124 (tp) REVERT: G 257 ASP cc_start: 0.7777 (t70) cc_final: 0.7283 (t0) REVERT: G 281 GLU cc_start: 0.7993 (pt0) cc_final: 0.7764 (pt0) REVERT: G 451 ILE cc_start: 0.7990 (mt) cc_final: 0.7682 (mm) REVERT: G 554 ARG cc_start: 0.7856 (mtp180) cc_final: 0.7623 (mtp-110) REVERT: G 652 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8438 (tttt) REVERT: H 57 TYR cc_start: 0.7390 (m-80) cc_final: 0.6574 (m-80) REVERT: H 67 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8229 (mm-40) REVERT: H 73 THR cc_start: 0.8396 (m) cc_final: 0.8054 (t) REVERT: H 75 TYR cc_start: 0.8219 (p90) cc_final: 0.7891 (p90) REVERT: I 93 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6976 (mp0) REVERT: I 109 ASN cc_start: 0.6862 (p0) cc_final: 0.6635 (p0) REVERT: I 116 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7192 (mt-10) REVERT: I 142 VAL cc_start: 0.8641 (t) cc_final: 0.8366 (p) REVERT: I 147 GLU cc_start: 0.6414 (mm-30) cc_final: 0.6095 (mm-30) REVERT: I 153 ILE cc_start: 0.8529 (mp) cc_final: 0.8252 (mt) REVERT: J 234 LYS cc_start: 0.8424 (mppt) cc_final: 0.7857 (mppt) REVERT: J 332 GLU cc_start: 0.7702 (tp30) cc_final: 0.7458 (tp30) REVERT: J 438 ARG cc_start: 0.8454 (ttm-80) cc_final: 0.8008 (mtt-85) REVERT: J 459 LYS cc_start: 0.8010 (mmtp) cc_final: 0.7450 (ttmm) REVERT: J 464 ARG cc_start: 0.7260 (mtm-85) cc_final: 0.6944 (mtm-85) REVERT: J 479 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: J 533 ILE cc_start: 0.8559 (tp) cc_final: 0.7749 (tp) REVERT: J 537 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7248 (mt-10) REVERT: J 679 MET cc_start: 0.5483 (ppp) cc_final: 0.4124 (ppp) REVERT: c 59 ILE cc_start: 0.8235 (mm) cc_final: 0.7504 (mm) REVERT: c 136 GLU cc_start: 0.7607 (tp30) cc_final: 0.7227 (tp30) REVERT: c 182 ARG cc_start: 0.7919 (mmm-85) cc_final: 0.7633 (mmm-85) REVERT: c 271 ASP cc_start: 0.7499 (m-30) cc_final: 0.7278 (m-30) REVERT: C 38 TYR cc_start: 0.7682 (m-10) cc_final: 0.7462 (m-80) REVERT: K 153 PHE cc_start: 0.7959 (m-80) cc_final: 0.7709 (m-80) REVERT: K 189 ARG cc_start: 0.7510 (mtt-85) cc_final: 0.7174 (mmt90) REVERT: K 192 THR cc_start: 0.8631 (m) cc_final: 0.8290 (p) REVERT: K 217 GLU cc_start: 0.6861 (tp30) cc_final: 0.6321 (tp30) REVERT: L 292 LEU cc_start: 0.9026 (mm) cc_final: 0.8297 (mm) REVERT: L 294 TRP cc_start: 0.7663 (t60) cc_final: 0.7260 (t60) REVERT: L 298 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7127 (mm-30) REVERT: L 301 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8323 (mtmm) REVERT: M 40 THR cc_start: 0.8686 (m) cc_final: 0.8238 (t) REVERT: M 57 PHE cc_start: 0.8539 (t80) cc_final: 0.8297 (t80) REVERT: M 92 TYR cc_start: 0.8518 (t80) cc_final: 0.7521 (t80) REVERT: M 95 GLU cc_start: 0.8218 (mt-10) cc_final: 0.8001 (mt-10) REVERT: M 155 GLN cc_start: 0.7901 (tp40) cc_final: 0.7502 (tm-30) REVERT: N 44 TYR cc_start: 0.7239 (t80) cc_final: 0.6873 (t80) REVERT: N 98 GLN cc_start: 0.8245 (mt0) cc_final: 0.7975 (mt0) REVERT: N 136 LYS cc_start: 0.8515 (mttt) cc_final: 0.8278 (mtpp) REVERT: N 142 VAL cc_start: 0.8907 (t) cc_final: 0.8687 (m) REVERT: N 147 GLU cc_start: 0.6875 (mt-10) cc_final: 0.6499 (mt-10) REVERT: N 185 GLU cc_start: 0.7219 (tt0) cc_final: 0.6828 (tt0) REVERT: N 199 GLU cc_start: 0.6327 (mm-30) cc_final: 0.6095 (mm-30) REVERT: O 281 GLU cc_start: 0.8160 (pt0) cc_final: 0.7702 (pp20) REVERT: O 347 HIS cc_start: 0.8838 (m170) cc_final: 0.8586 (m170) REVERT: O 442 ARG cc_start: 0.8513 (ttt90) cc_final: 0.8192 (ttt180) REVERT: O 502 TYR cc_start: 0.5739 (p90) cc_final: 0.4726 (p90) REVERT: O 641 LYS cc_start: 0.8224 (mmtt) cc_final: 0.8014 (mmtt) REVERT: O 692 MET cc_start: 0.7680 (mtm) cc_final: 0.7318 (mtm) REVERT: P 43 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7301 (mtm-85) REVERT: P 180 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7679 (mt-10) REVERT: P 250 TYR cc_start: 0.5745 (t80) cc_final: 0.5348 (t80) REVERT: Q 105 TYR cc_start: 0.7774 (t80) cc_final: 0.7277 (t80) REVERT: Q 116 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6819 (mt-10) REVERT: Q 151 GLU cc_start: 0.6803 (tp30) cc_final: 0.6024 (tp30) REVERT: Q 158 ARG cc_start: 0.6863 (mtt-85) cc_final: 0.6570 (ttm110) REVERT: R 211 GLN cc_start: 0.7821 (mp10) cc_final: 0.7549 (mp-120) REVERT: R 280 TYR cc_start: 0.6323 (m-10) cc_final: 0.5926 (m-10) REVERT: R 287 LYS cc_start: 0.8368 (pttm) cc_final: 0.7963 (pttm) REVERT: R 313 ASN cc_start: 0.8354 (t0) cc_final: 0.7978 (t0) REVERT: R 316 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7966 (tm-30) REVERT: R 353 ARG cc_start: 0.7782 (ttp80) cc_final: 0.7213 (ttt-90) REVERT: R 433 CYS cc_start: 0.7747 (t) cc_final: 0.7523 (p) REVERT: R 531 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7502 (mm-40) REVERT: R 556 ASN cc_start: 0.8691 (m-40) cc_final: 0.8212 (m-40) REVERT: R 641 LYS cc_start: 0.8006 (pttm) cc_final: 0.7757 (pttm) REVERT: d 73 THR cc_start: 0.9093 (m) cc_final: 0.8660 (t) REVERT: d 78 ASN cc_start: 0.7866 (p0) cc_final: 0.6809 (p0) REVERT: d 81 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6857 (mt-10) REVERT: d 92 MET cc_start: 0.7771 (mtp) cc_final: 0.7556 (mtp) REVERT: d 135 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8148 (mmtt) REVERT: d 180 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7319 (mm-30) REVERT: d 183 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8357 (ptpp) REVERT: d 262 TYR cc_start: 0.8647 (t80) cc_final: 0.8395 (t80) REVERT: d 269 ASN cc_start: 0.8569 (t0) cc_final: 0.8256 (t0) outliers start: 12 outliers final: 4 residues processed: 1192 average time/residue: 0.2575 time to fit residues: 470.1499 Evaluate side-chains 1132 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1127 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain J residue 479 GLU Chi-restraints excluded: chain K residue 155 CYS Chi-restraints excluded: chain P residue 248 THR Chi-restraints excluded: chain d residue 23 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 0.0670 chunk 388 optimal weight: 0.1980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.3980 chunk 401 optimal weight: 0.7980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS E 31 GLN ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN F 33 HIS F 54 HIS G 323 GLN G 503 GLN G 531 GLN J 271 HIS J 286 GLN J 342 GLN J 531 GLN J 541 ASN J 547 GLN c 78 ASN C 39 HIS K 202 GLN L 297 ASN M 195 ASN N 77 HIS ** N 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 657 ASN Q 33 HIS Q 120 HIS Q 157 HIS ** R 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 342 GLN R 350 GLN ** R 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 95 GLN d 146 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.135091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.114233 restraints weight = 73357.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.118100 restraints weight = 35036.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.120695 restraints weight = 21182.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.122147 restraints weight = 14769.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.123480 restraints weight = 11738.568| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 34806 Z= 0.167 Angle : 0.732 14.360 47180 Z= 0.380 Chirality : 0.046 0.253 4964 Planarity : 0.006 0.067 6150 Dihedral : 5.595 45.991 4643 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.43 % Favored : 95.35 % Rotamer: Outliers : 3.54 % Allowed : 17.59 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 4110 helix: -0.14 (0.15), residues: 1140 sheet: -1.27 (0.17), residues: 818 loop : -0.69 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 373 TYR 0.023 0.002 TYR H 219 PHE 0.030 0.002 PHE N 50 TRP 0.030 0.002 TRP D 294 HIS 0.011 0.001 HIS F 120 Details of bonding type rmsd covalent geometry : bond 0.00365 (34806) covalent geometry : angle 0.73170 (47180) hydrogen bonds : bond 0.04710 ( 1325) hydrogen bonds : angle 6.22886 ( 3786) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1318 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1189 time to evaluate : 1.419 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: 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: A 20 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7096 (tm-30) REVERT: B 146 LEU cc_start: 0.7428 (mt) cc_final: 0.7223 (mm) REVERT: B 215 VAL cc_start: 0.8703 (t) cc_final: 0.8422 (m) REVERT: B 226 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7052 (mt-10) REVERT: B 253 ASP cc_start: 0.7766 (t70) cc_final: 0.7534 (t0) REVERT: B 256 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8346 (tt) REVERT: D 294 TRP cc_start: 0.7643 (t60) cc_final: 0.7332 (t60) REVERT: D 301 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8103 (mtmp) REVERT: E 44 ARG cc_start: 0.7790 (ttp-170) cc_final: 0.7495 (ttp-170) REVERT: E 74 MET cc_start: 0.6973 (mmp) cc_final: 0.6044 (mmm) REVERT: E 123 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6652 (mmp80) REVERT: E 158 LYS cc_start: 0.8115 (ptmt) cc_final: 0.7548 (pttm) REVERT: E 175 GLU cc_start: 0.7278 (pp20) cc_final: 0.6517 (pp20) REVERT: E 186 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6497 (mm) REVERT: F 59 TYR cc_start: 0.6986 (t80) cc_final: 0.6727 (t80) REVERT: F 67 TYR cc_start: 0.7280 (t80) cc_final: 0.6318 (t80) REVERT: F 93 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6885 (mm-30) REVERT: F 98 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7456 (mm-40) REVERT: F 142 VAL cc_start: 0.8747 (t) cc_final: 0.8151 (m) REVERT: F 147 GLU cc_start: 0.7249 (tt0) cc_final: 0.6794 (tt0) REVERT: F 156 ASN cc_start: 0.8199 (p0) cc_final: 0.7800 (p0) REVERT: F 164 MET cc_start: 0.6952 (ttm) cc_final: 0.6737 (mtm) REVERT: G 251 ILE cc_start: 0.8142 (tt) cc_final: 0.7926 (tp) REVERT: G 257 ASP cc_start: 0.7986 (t70) cc_final: 0.7511 (t0) REVERT: G 276 MET cc_start: 0.6872 (mmm) cc_final: 0.6206 (mmm) REVERT: G 281 GLU cc_start: 0.8147 (pt0) cc_final: 0.7554 (pp20) REVERT: G 284 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7178 (mm-30) REVERT: G 332 GLU cc_start: 0.8138 (tp30) cc_final: 0.7535 (tp30) REVERT: G 335 ARG cc_start: 0.7373 (tpp80) cc_final: 0.6926 (tpp80) REVERT: G 345 ASP cc_start: 0.7542 (m-30) cc_final: 0.7286 (m-30) REVERT: G 350 GLN cc_start: 0.8222 (tt0) cc_final: 0.7926 (tp40) REVERT: G 351 ARG cc_start: 0.7448 (ttp-170) cc_final: 0.6823 (ttp-170) REVERT: G 373 ARG cc_start: 0.7608 (mtm-85) cc_final: 0.7042 (mtm-85) REVERT: G 428 TYR cc_start: 0.8244 (m-80) cc_final: 0.7619 (m-10) REVERT: G 451 ILE cc_start: 0.8265 (mt) cc_final: 0.7847 (mm) REVERT: G 503 GLN cc_start: 0.7934 (pt0) cc_final: 0.6650 (pt0) REVERT: G 668 GLN cc_start: 0.8168 (mp10) cc_final: 0.7835 (mp10) REVERT: G 688 GLN cc_start: 0.8563 (tp40) cc_final: 0.7861 (tp40) REVERT: G 692 MET cc_start: 0.7409 (mmp) cc_final: 0.7143 (mmp) REVERT: H 25 ARG cc_start: 0.8534 (ttm-80) cc_final: 0.8293 (ttm-80) REVERT: H 57 TYR cc_start: 0.7321 (m-80) cc_final: 0.5831 (m-80) REVERT: H 71 ARG cc_start: 0.7273 (ptt180) cc_final: 0.6911 (ptt180) REVERT: H 230 MET cc_start: 0.8443 (mmm) cc_final: 0.8198 (mmt) REVERT: H 260 TYR cc_start: 0.8896 (p90) cc_final: 0.8640 (p90) REVERT: H 270 MET cc_start: 0.7112 (mmm) cc_final: 0.6877 (mmm) REVERT: I 59 TYR cc_start: 0.6479 (m-80) cc_final: 0.6229 (m-80) REVERT: I 104 VAL cc_start: 0.7658 (t) cc_final: 0.7346 (p) REVERT: I 111 ASP cc_start: 0.7821 (m-30) cc_final: 0.7426 (m-30) REVERT: I 138 VAL cc_start: 0.8317 (t) cc_final: 0.8115 (t) REVERT: I 142 VAL cc_start: 0.8709 (t) cc_final: 0.8348 (p) REVERT: I 147 GLU cc_start: 0.6677 (mm-30) cc_final: 0.6313 (mm-30) REVERT: I 153 ILE cc_start: 0.8666 (mp) cc_final: 0.8255 (mt) REVERT: J 216 TYR cc_start: 0.8281 (t80) cc_final: 0.7984 (t80) REVERT: J 256 GLN cc_start: 0.8324 (mt0) cc_final: 0.7957 (mm110) REVERT: J 257 ASP cc_start: 0.7802 (t0) cc_final: 0.7559 (t0) REVERT: J 260 MET cc_start: 0.7843 (tmm) cc_final: 0.7575 (tmm) REVERT: J 331 ASP cc_start: 0.7708 (t0) cc_final: 0.7366 (t0) REVERT: J 438 ARG cc_start: 0.8588 (ttm-80) cc_final: 0.8161 (mtt-85) REVERT: J 458 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8765 (ttmm) REVERT: J 459 LYS cc_start: 0.8550 (mmtp) cc_final: 0.8314 (tttt) REVERT: J 554 ARG cc_start: 0.8733 (mtp85) cc_final: 0.8509 (mtp85) REVERT: J 611 GLN cc_start: 0.8060 (pt0) cc_final: 0.7857 (pt0) REVERT: J 679 MET cc_start: 0.5592 (ppp) cc_final: 0.4667 (tmm) REVERT: c 59 ILE cc_start: 0.8603 (mm) cc_final: 0.8265 (mm) REVERT: c 96 ILE cc_start: 0.8782 (pt) cc_final: 0.8417 (pt) REVERT: c 136 GLU cc_start: 0.7827 (tp30) cc_final: 0.7489 (tp30) REVERT: c 142 SER cc_start: 0.8510 (m) cc_final: 0.7845 (p) REVERT: c 145 ASP cc_start: 0.8203 (t0) cc_final: 0.7360 (t0) REVERT: c 191 ARG cc_start: 0.7319 (mtp180) cc_final: 0.6954 (mtp180) REVERT: c 248 THR cc_start: 0.8723 (m) cc_final: 0.8381 (t) REVERT: c 258 TYR cc_start: 0.8090 (p90) cc_final: 0.7642 (p90) REVERT: c 270 MET cc_start: 0.7537 (ppp) cc_final: 0.7293 (ppp) REVERT: c 271 ASP cc_start: 0.8009 (m-30) cc_final: 0.7405 (m-30) REVERT: C 7 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7276 (tppt) REVERT: K 153 PHE cc_start: 0.8211 (m-80) cc_final: 0.7833 (m-80) REVERT: K 189 ARG cc_start: 0.7614 (mtt-85) cc_final: 0.7216 (mmt90) REVERT: K 192 THR cc_start: 0.8653 (m) cc_final: 0.8255 (p) REVERT: K 217 GLU cc_start: 0.7066 (tp30) cc_final: 0.6497 (mm-30) REVERT: K 258 ASN cc_start: 0.8478 (t0) cc_final: 0.8273 (t0) REVERT: L 297 ASN cc_start: 0.8391 (m110) cc_final: 0.8128 (m110) REVERT: L 301 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8492 (mtmm) REVERT: M 40 THR cc_start: 0.8712 (m) cc_final: 0.8237 (t) REVERT: M 95 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7980 (mt-10) REVERT: M 139 ILE cc_start: 0.8503 (mt) cc_final: 0.8155 (tt) REVERT: M 158 LYS cc_start: 0.8257 (mttt) cc_final: 0.7770 (mttt) REVERT: M 191 TRP cc_start: 0.7985 (t-100) cc_final: 0.7675 (t-100) REVERT: N 25 ASN cc_start: 0.5925 (OUTLIER) cc_final: 0.5709 (t0) REVERT: N 98 GLN cc_start: 0.8332 (mt0) cc_final: 0.7842 (mt0) REVERT: N 136 LYS cc_start: 0.8557 (mttt) cc_final: 0.8272 (mtpp) REVERT: N 182 GLN cc_start: 0.7845 (tp40) cc_final: 0.7493 (tm-30) REVERT: N 185 GLU cc_start: 0.7381 (tt0) cc_final: 0.6876 (tt0) REVERT: O 241 ASP cc_start: 0.5746 (m-30) cc_final: 0.5239 (p0) REVERT: O 252 GLU cc_start: 0.7714 (mp0) cc_final: 0.7484 (mp0) REVERT: O 281 GLU cc_start: 0.8510 (pt0) cc_final: 0.7816 (pp20) REVERT: O 284 GLU cc_start: 0.7912 (tp30) cc_final: 0.7644 (tp30) REVERT: O 347 HIS cc_start: 0.8788 (m170) cc_final: 0.8470 (m170) REVERT: O 350 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7160 (tm-30) REVERT: O 371 GLU cc_start: 0.6935 (tp30) cc_final: 0.5789 (tm-30) REVERT: O 438 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7662 (mtp85) REVERT: O 502 TYR cc_start: 0.6014 (p90) cc_final: 0.4771 (p90) REVERT: O 688 GLN cc_start: 0.8606 (tp40) cc_final: 0.8190 (tm-30) REVERT: O 692 MET cc_start: 0.7664 (mtm) cc_final: 0.6146 (mtm) REVERT: P 10 LEU cc_start: 0.7218 (mm) cc_final: 0.6538 (mt) REVERT: P 33 MET cc_start: 0.8144 (mmt) cc_final: 0.7892 (mmp) REVERT: P 40 ARG cc_start: 0.7810 (ttm110) cc_final: 0.7520 (ttm-80) REVERT: P 43 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7354 (mtm-85) REVERT: P 78 ASN cc_start: 0.7324 (t0) cc_final: 0.7005 (t0) REVERT: P 180 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7733 (mt-10) REVERT: Q 116 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6830 (mt-10) REVERT: Q 125 GLN cc_start: 0.8616 (tp40) cc_final: 0.8369 (tp40) REVERT: Q 138 VAL cc_start: 0.8445 (t) cc_final: 0.8110 (m) REVERT: Q 151 GLU cc_start: 0.7004 (tp30) cc_final: 0.6542 (tp30) REVERT: Q 156 ASN cc_start: 0.8005 (m110) cc_final: 0.7643 (m-40) REVERT: Q 173 LYS cc_start: 0.8508 (ptpp) cc_final: 0.8168 (ptpp) REVERT: R 238 LYS cc_start: 0.8640 (tttp) cc_final: 0.8387 (tttp) REVERT: R 249 ASP cc_start: 0.8253 (t0) cc_final: 0.8049 (t0) REVERT: R 259 LYS cc_start: 0.8947 (mmtp) cc_final: 0.8730 (mttp) REVERT: R 284 GLU cc_start: 0.7432 (tp30) cc_final: 0.7120 (tp30) REVERT: R 313 ASN cc_start: 0.8383 (t0) cc_final: 0.7877 (t0) REVERT: R 316 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7996 (tm-30) REVERT: R 322 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7782 (tm-30) REVERT: R 373 ARG cc_start: 0.7059 (ptp90) cc_final: 0.6598 (ptp90) REVERT: R 418 LYS cc_start: 0.8049 (ptmm) cc_final: 0.7773 (ptmm) REVERT: R 438 ARG cc_start: 0.8230 (tpp80) cc_final: 0.7995 (mtt-85) REVERT: R 556 ASN cc_start: 0.8709 (m-40) cc_final: 0.8348 (m-40) REVERT: R 619 GLN cc_start: 0.8031 (tp40) cc_final: 0.7626 (tp40) REVERT: R 640 LYS cc_start: 0.8672 (tptt) cc_final: 0.8459 (tptt) REVERT: R 681 ASP cc_start: 0.6587 (OUTLIER) cc_final: 0.6114 (m-30) REVERT: d 2 ASP cc_start: 0.8148 (t0) cc_final: 0.7762 (t0) REVERT: d 37 ARG cc_start: 0.8712 (ttp80) cc_final: 0.8500 (ttp80) REVERT: d 38 ASP cc_start: 0.8015 (m-30) cc_final: 0.7520 (m-30) REVERT: d 43 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7758 (ttp80) REVERT: d 81 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6880 (mt-10) REVERT: d 135 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8148 (mmtt) REVERT: d 170 ASN cc_start: 0.7622 (t0) cc_final: 0.7100 (t0) REVERT: d 180 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7378 (mm-30) REVERT: d 183 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8381 (ptpp) REVERT: d 228 ILE cc_start: 0.8829 (mt) cc_final: 0.8535 (tt) REVERT: d 248 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8651 (p) REVERT: d 269 ASN cc_start: 0.8797 (t0) cc_final: 0.8500 (t0) outliers start: 129 outliers final: 79 residues processed: 1236 average time/residue: 0.2591 time to fit residues: 490.0224 Evaluate side-chains 1228 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 1141 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 588 VAL Chi-restraints excluded: chain G residue 605 ILE Chi-restraints excluded: chain G residue 617 ILE Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 458 LYS Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 92 MET Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 261 ILE Chi-restraints excluded: chain c residue 265 THR Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain K residue 222 ARG Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain M residue 193 MET Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 155 LEU Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 351 ARG Chi-restraints excluded: chain O residue 433 CYS Chi-restraints excluded: chain O residue 435 VAL Chi-restraints excluded: chain O residue 540 SER Chi-restraints excluded: chain P residue 67 GLN Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 134 ILE Chi-restraints excluded: chain P residue 261 ILE Chi-restraints excluded: chain P residue 271 ASP Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 157 HIS Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 180 CYS Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 654 CYS Chi-restraints excluded: chain R residue 681 ASP Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 95 GLN Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 16 optimal weight: 0.9980 chunk 346 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 371 optimal weight: 0.6980 chunk 318 optimal weight: 0.7980 chunk 228 optimal weight: 0.7980 chunk 121 optimal weight: 0.0370 chunk 174 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 387 optimal weight: 0.0470 chunk 86 optimal weight: 1.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 56 ASN E 162 ASN ** F 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 531 GLN G 547 GLN J 323 GLN J 350 GLN c 257 ASN M 162 ASN ** N 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 286 GLN O 486 GLN O 531 GLN Q 157 HIS ** R 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.133983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113034 restraints weight = 72745.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.116902 restraints weight = 34849.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.119399 restraints weight = 21134.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.121179 restraints weight = 14902.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.122354 restraints weight = 11409.029| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34806 Z= 0.158 Angle : 0.684 13.591 47180 Z= 0.353 Chirality : 0.045 0.226 4964 Planarity : 0.005 0.062 6150 Dihedral : 5.203 41.859 4634 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.48 % Favored : 95.33 % Rotamer: Outliers : 3.46 % Allowed : 18.85 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.13), residues: 4110 helix: 0.09 (0.15), residues: 1136 sheet: -1.14 (0.17), residues: 788 loop : -0.63 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 41 TYR 0.030 0.002 TYR I 44 PHE 0.026 0.002 PHE N 50 TRP 0.020 0.001 TRP M 187 HIS 0.015 0.001 HIS Q 157 Details of bonding type rmsd covalent geometry : bond 0.00346 (34806) covalent geometry : angle 0.68439 (47180) hydrogen bonds : bond 0.04246 ( 1325) hydrogen bonds : angle 5.84776 ( 3786) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 1162 time to evaluate : 1.138 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: 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: A 3 THR cc_start: 0.8805 (p) cc_final: 0.8363 (m) REVERT: A 20 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7067 (tm-30) REVERT: B 215 VAL cc_start: 0.8770 (t) cc_final: 0.8437 (m) REVERT: B 222 ARG cc_start: 0.7430 (mtm110) cc_final: 0.7168 (mtm110) REVERT: B 226 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7067 (mt-10) REVERT: B 253 ASP cc_start: 0.7826 (t70) cc_final: 0.7406 (t0) REVERT: D 294 TRP cc_start: 0.7660 (t60) cc_final: 0.7275 (t60) REVERT: D 301 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8161 (mtmt) REVERT: D 307 MET cc_start: 0.7071 (tpp) cc_final: 0.6803 (tpp) REVERT: E 28 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7178 (mt-10) REVERT: E 44 ARG cc_start: 0.7760 (ttp-170) cc_final: 0.7527 (ttp-170) REVERT: E 74 MET cc_start: 0.6998 (mmp) cc_final: 0.6611 (mmp) REVERT: E 92 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7629 (t80) REVERT: E 97 MET cc_start: 0.5592 (mmt) cc_final: 0.5237 (mmt) REVERT: E 106 LYS cc_start: 0.8316 (mttm) cc_final: 0.8116 (mttm) REVERT: E 123 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6775 (mmp80) REVERT: E 158 LYS cc_start: 0.8113 (ptmt) cc_final: 0.7854 (ptmt) REVERT: E 175 GLU cc_start: 0.7244 (pp20) cc_final: 0.6956 (pp20) REVERT: F 59 TYR cc_start: 0.7033 (t80) cc_final: 0.6759 (t80) REVERT: F 67 TYR cc_start: 0.7404 (t80) cc_final: 0.6449 (t80) REVERT: F 98 GLN cc_start: 0.8305 (mm-40) cc_final: 0.7402 (mm-40) REVERT: F 142 VAL cc_start: 0.8763 (t) cc_final: 0.8137 (m) REVERT: F 147 GLU cc_start: 0.7360 (tt0) cc_final: 0.6806 (tt0) REVERT: F 156 ASN cc_start: 0.8197 (p0) cc_final: 0.7719 (p0) REVERT: G 251 ILE cc_start: 0.8074 (tt) cc_final: 0.7747 (tp) REVERT: G 257 ASP cc_start: 0.8042 (t70) cc_final: 0.7495 (t0) REVERT: G 276 MET cc_start: 0.6858 (mmm) cc_final: 0.6225 (mmm) REVERT: G 281 GLU cc_start: 0.8130 (pt0) cc_final: 0.7522 (pp20) REVERT: G 284 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7202 (mm-30) REVERT: G 316 GLU cc_start: 0.8267 (tt0) cc_final: 0.7957 (tt0) REVERT: G 322 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7936 (mm-30) REVERT: G 331 ASP cc_start: 0.8294 (t70) cc_final: 0.7980 (t0) REVERT: G 332 GLU cc_start: 0.8185 (tp30) cc_final: 0.7867 (tp30) REVERT: G 335 ARG cc_start: 0.7197 (tpp80) cc_final: 0.6763 (tpp80) REVERT: G 345 ASP cc_start: 0.7597 (m-30) cc_final: 0.7297 (m-30) REVERT: G 350 GLN cc_start: 0.8221 (tt0) cc_final: 0.7800 (tp40) REVERT: G 351 ARG cc_start: 0.7478 (ttp-170) cc_final: 0.6770 (ttp-170) REVERT: G 373 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7245 (mtm-85) REVERT: G 428 TYR cc_start: 0.8240 (m-80) cc_final: 0.7613 (m-10) REVERT: G 451 ILE cc_start: 0.8310 (mt) cc_final: 0.7906 (mm) REVERT: G 503 GLN cc_start: 0.7932 (pt0) cc_final: 0.7514 (pt0) REVERT: G 656 GLU cc_start: 0.7738 (mp0) cc_final: 0.7336 (pm20) REVERT: G 688 GLN cc_start: 0.8563 (tp40) cc_final: 0.7717 (tp40) REVERT: G 692 MET cc_start: 0.7478 (mmp) cc_final: 0.7174 (mmp) REVERT: H 57 TYR cc_start: 0.7489 (m-80) cc_final: 0.6476 (m-80) REVERT: H 94 MET cc_start: 0.7589 (tmm) cc_final: 0.7162 (tmm) REVERT: H 95 GLN cc_start: 0.7807 (mt0) cc_final: 0.7486 (mm110) REVERT: H 145 ASP cc_start: 0.7786 (t0) cc_final: 0.7501 (t0) REVERT: I 44 TYR cc_start: 0.6591 (t80) cc_final: 0.6357 (t80) REVERT: I 104 VAL cc_start: 0.7721 (t) cc_final: 0.7374 (p) REVERT: I 138 VAL cc_start: 0.8404 (t) cc_final: 0.8060 (t) REVERT: I 142 VAL cc_start: 0.8768 (t) cc_final: 0.8387 (p) REVERT: I 147 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6597 (mm-30) REVERT: I 153 ILE cc_start: 0.8734 (mp) cc_final: 0.8309 (mt) REVERT: J 256 GLN cc_start: 0.8317 (mt0) cc_final: 0.8027 (mm110) REVERT: J 257 ASP cc_start: 0.7739 (t0) cc_final: 0.7430 (t0) REVERT: J 260 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7480 (tmm) REVERT: J 362 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7336 (mt-10) REVERT: J 438 ARG cc_start: 0.8592 (ttm-80) cc_final: 0.8151 (mtt-85) REVERT: J 456 LYS cc_start: 0.8527 (mtmm) cc_final: 0.8308 (mtmm) REVERT: J 458 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8893 (ttpp) REVERT: J 464 ARG cc_start: 0.7361 (mtm-85) cc_final: 0.7126 (mtm-85) REVERT: J 618 PRO cc_start: 0.8758 (Cg_endo) cc_final: 0.8437 (Cg_exo) REVERT: c 57 TYR cc_start: 0.8261 (m-80) cc_final: 0.8051 (m-80) REVERT: c 59 ILE cc_start: 0.8689 (mm) cc_final: 0.8304 (mm) REVERT: c 96 ILE cc_start: 0.8762 (pt) cc_final: 0.8332 (pt) REVERT: c 136 GLU cc_start: 0.7870 (tp30) cc_final: 0.7596 (tp30) REVERT: c 142 SER cc_start: 0.8523 (m) cc_final: 0.7878 (p) REVERT: c 170 ASN cc_start: 0.7536 (t0) cc_final: 0.7302 (t0) REVERT: c 191 ARG cc_start: 0.7388 (mtp180) cc_final: 0.7094 (mtp180) REVERT: c 248 THR cc_start: 0.8666 (m) cc_final: 0.8379 (t) REVERT: c 258 TYR cc_start: 0.8187 (p90) cc_final: 0.7760 (p90) REVERT: c 262 TYR cc_start: 0.8923 (t80) cc_final: 0.8223 (t80) REVERT: c 270 MET cc_start: 0.7618 (ppp) cc_final: 0.7303 (ppp) REVERT: c 271 ASP cc_start: 0.8040 (m-30) cc_final: 0.7316 (m-30) REVERT: K 183 ASP cc_start: 0.6369 (t0) cc_final: 0.5953 (t0) REVERT: K 217 GLU cc_start: 0.7198 (tp30) cc_final: 0.6862 (tp30) REVERT: K 258 ASN cc_start: 0.8559 (t0) cc_final: 0.8213 (t0) REVERT: L 292 LEU cc_start: 0.8955 (mm) cc_final: 0.8448 (mm) REVERT: L 294 TRP cc_start: 0.7635 (t60) cc_final: 0.7395 (t60) REVERT: L 297 ASN cc_start: 0.8416 (m110) cc_final: 0.8125 (m110) REVERT: L 301 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8468 (mtmm) REVERT: L 307 MET cc_start: 0.7510 (tpp) cc_final: 0.7241 (tpp) REVERT: M 27 GLU cc_start: 0.7632 (tt0) cc_final: 0.7360 (tm-30) REVERT: M 88 LYS cc_start: 0.7836 (mmmm) cc_final: 0.7419 (tppp) REVERT: M 94 LYS cc_start: 0.8135 (mttt) cc_final: 0.7910 (mttt) REVERT: M 95 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7923 (mt-10) REVERT: M 139 ILE cc_start: 0.8513 (mt) cc_final: 0.8195 (tt) REVERT: M 158 LYS cc_start: 0.8325 (mttt) cc_final: 0.7960 (mttt) REVERT: N 25 ASN cc_start: 0.6053 (OUTLIER) cc_final: 0.5779 (t0) REVERT: N 91 GLU cc_start: 0.7316 (mp0) cc_final: 0.7021 (mp0) REVERT: N 98 GLN cc_start: 0.8313 (mt0) cc_final: 0.7820 (mt0) REVERT: N 136 LYS cc_start: 0.8572 (mttt) cc_final: 0.8281 (mtpp) REVERT: N 185 GLU cc_start: 0.7448 (tt0) cc_final: 0.6914 (tt0) REVERT: O 241 ASP cc_start: 0.5736 (m-30) cc_final: 0.5246 (p0) REVERT: O 281 GLU cc_start: 0.8510 (pt0) cc_final: 0.7885 (pp20) REVERT: O 331 ASP cc_start: 0.8557 (p0) cc_final: 0.8345 (p0) REVERT: O 347 HIS cc_start: 0.8841 (m170) cc_final: 0.8572 (m170) REVERT: O 350 GLN cc_start: 0.8332 (tm-30) cc_final: 0.7230 (tm-30) REVERT: O 371 GLU cc_start: 0.7005 (tp30) cc_final: 0.5864 (tm-30) REVERT: O 438 ARG cc_start: 0.8112 (ttm-80) cc_final: 0.7881 (mtp85) REVERT: O 502 TYR cc_start: 0.6090 (p90) cc_final: 0.4740 (p90) REVERT: O 688 GLN cc_start: 0.8567 (tp40) cc_final: 0.8247 (tm-30) REVERT: O 692 MET cc_start: 0.7771 (mtm) cc_final: 0.6272 (mtm) REVERT: P 1 MET cc_start: 0.5085 (ptt) cc_final: 0.4569 (ptp) REVERT: P 10 LEU cc_start: 0.6870 (mm) cc_final: 0.6634 (mt) REVERT: P 28 LEU cc_start: 0.8509 (tp) cc_final: 0.8050 (mm) REVERT: P 33 MET cc_start: 0.8136 (mmt) cc_final: 0.7787 (mmp) REVERT: P 43 ARG cc_start: 0.7929 (mtm-85) cc_final: 0.7717 (mtm-85) REVERT: P 67 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7630 (mt0) REVERT: P 78 ASN cc_start: 0.7361 (t0) cc_final: 0.6944 (t0) REVERT: P 180 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7716 (mt-10) REVERT: P 250 TYR cc_start: 0.5884 (t80) cc_final: 0.5414 (t80) REVERT: P 267 GLU cc_start: 0.6938 (mp0) cc_final: 0.6078 (mp0) REVERT: Q 106 TYR cc_start: 0.8008 (m-80) cc_final: 0.7430 (m-80) REVERT: Q 116 GLU cc_start: 0.7513 (mt-10) cc_final: 0.6920 (mt-10) REVERT: Q 138 VAL cc_start: 0.8470 (t) cc_final: 0.8134 (m) REVERT: Q 151 GLU cc_start: 0.6967 (tp30) cc_final: 0.6369 (tp30) REVERT: Q 156 ASN cc_start: 0.8177 (m110) cc_final: 0.7176 (m-40) REVERT: Q 173 LYS cc_start: 0.8462 (ptpp) cc_final: 0.8023 (ptpp) REVERT: Q 181 GLU cc_start: 0.7535 (tt0) cc_final: 0.7308 (tt0) REVERT: R 207 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.6362 (mp0) REVERT: R 211 GLN cc_start: 0.8013 (mt0) cc_final: 0.7807 (mm-40) REVERT: R 212 ASN cc_start: 0.7424 (t0) cc_final: 0.7087 (t0) REVERT: R 238 LYS cc_start: 0.8709 (tttp) cc_final: 0.8440 (tttp) REVERT: R 249 ASP cc_start: 0.8321 (t0) cc_final: 0.8075 (t0) REVERT: R 259 LYS cc_start: 0.8984 (mmtp) cc_final: 0.8726 (mttp) REVERT: R 260 MET cc_start: 0.7793 (tpp) cc_final: 0.7582 (mmm) REVERT: R 284 GLU cc_start: 0.7509 (tp30) cc_final: 0.7192 (tp30) REVERT: R 313 ASN cc_start: 0.8316 (t0) cc_final: 0.7573 (t0) REVERT: R 316 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7819 (tm-30) REVERT: R 322 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7588 (tm-30) REVERT: R 334 TYR cc_start: 0.8095 (t80) cc_final: 0.7684 (t80) REVERT: R 433 CYS cc_start: 0.7632 (p) cc_final: 0.7394 (p) REVERT: R 438 ARG cc_start: 0.8586 (tpp80) cc_final: 0.7994 (mtt-85) REVERT: R 464 ARG cc_start: 0.7375 (mtm-85) cc_final: 0.7049 (mtm-85) REVERT: R 470 ILE cc_start: 0.8847 (mm) cc_final: 0.8301 (pt) REVERT: R 530 ILE cc_start: 0.8887 (mm) cc_final: 0.8508 (tp) REVERT: R 556 ASN cc_start: 0.8777 (m-40) cc_final: 0.8383 (m-40) REVERT: R 619 GLN cc_start: 0.8010 (tp40) cc_final: 0.7584 (tp-100) REVERT: R 640 LYS cc_start: 0.8661 (tptt) cc_final: 0.8364 (tptm) REVERT: R 679 MET cc_start: 0.4552 (tmm) cc_final: 0.3637 (tmm) REVERT: d 28 LEU cc_start: 0.8620 (tp) cc_final: 0.8396 (tt) REVERT: d 38 ASP cc_start: 0.8073 (m-30) cc_final: 0.7578 (m-30) REVERT: d 43 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7996 (ttp-110) REVERT: d 81 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6906 (mt-10) REVERT: d 170 ASN cc_start: 0.7651 (t0) cc_final: 0.7176 (t0) REVERT: d 180 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7327 (mm-30) REVERT: d 183 LYS cc_start: 0.8712 (mtmt) cc_final: 0.8393 (ptpp) REVERT: d 230 MET cc_start: 0.7124 (mmm) cc_final: 0.6860 (mmm) REVERT: d 248 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8676 (p) REVERT: d 269 ASN cc_start: 0.8813 (t0) cc_final: 0.8565 (t0) outliers start: 126 outliers final: 83 residues processed: 1210 average time/residue: 0.2516 time to fit residues: 464.5469 Evaluate side-chains 1223 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 1132 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 588 VAL Chi-restraints excluded: chain G residue 617 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 268 LYS Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain J residue 458 LYS Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain c residue 67 GLN Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 180 GLU Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 257 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain L residue 308 VAL Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 15 THR Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 433 CYS Chi-restraints excluded: chain O residue 435 VAL Chi-restraints excluded: chain O residue 540 SER Chi-restraints excluded: chain O residue 647 ILE Chi-restraints excluded: chain P residue 67 GLN Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 271 ASP Chi-restraints excluded: chain Q residue 157 HIS Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 456 LYS Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 654 CYS Chi-restraints excluded: chain R residue 677 THR Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Chi-restraints excluded: chain d residue 254 ARG Chi-restraints excluded: chain d residue 257 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 281 optimal weight: 0.0570 chunk 39 optimal weight: 1.9990 chunk 308 optimal weight: 1.9990 chunk 366 optimal weight: 0.0970 chunk 191 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 373 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 300 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 547 GLN G 552 GLN G 688 GLN J 323 GLN J 350 GLN c 109 HIS c 234 ASN c 269 ASN M 162 ASN N 157 HIS N 183 HIS O 323 GLN O 531 GLN Q 157 HIS ** R 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 257 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.130975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.109833 restraints weight = 72559.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.113677 restraints weight = 34837.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116260 restraints weight = 21215.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.117910 restraints weight = 14901.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.118880 restraints weight = 11575.916| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34806 Z= 0.195 Angle : 0.679 13.331 47180 Z= 0.351 Chirality : 0.044 0.223 4964 Planarity : 0.005 0.060 6150 Dihedral : 5.112 43.474 4634 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.70 % Favored : 95.11 % Rotamer: Outliers : 3.90 % Allowed : 19.73 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.13), residues: 4110 helix: 0.18 (0.15), residues: 1142 sheet: -1.14 (0.17), residues: 798 loop : -0.55 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 41 TYR 0.030 0.002 TYR I 44 PHE 0.017 0.002 PHE E 141 TRP 0.021 0.002 TRP M 187 HIS 0.020 0.001 HIS Q 157 Details of bonding type rmsd covalent geometry : bond 0.00427 (34806) covalent geometry : angle 0.67948 (47180) hydrogen bonds : bond 0.04112 ( 1325) hydrogen bonds : angle 5.67563 ( 3786) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1302 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 1160 time to evaluate : 1.101 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: 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: A 3 THR cc_start: 0.8848 (p) cc_final: 0.8547 (m) REVERT: A 7 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7349 (mptp) REVERT: A 20 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7250 (tm-30) REVERT: A 21 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8475 (p) REVERT: B 146 LEU cc_start: 0.7404 (mt) cc_final: 0.7125 (mt) REVERT: B 150 ASP cc_start: 0.7943 (t0) cc_final: 0.7339 (t0) REVERT: B 215 VAL cc_start: 0.8721 (t) cc_final: 0.8439 (m) REVERT: B 226 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7035 (mt-10) REVERT: D 294 TRP cc_start: 0.7788 (t60) cc_final: 0.7141 (t60) REVERT: D 298 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7682 (mt-10) REVERT: D 301 LYS cc_start: 0.8770 (mtmt) cc_final: 0.8310 (mtmp) REVERT: D 307 MET cc_start: 0.7147 (tpp) cc_final: 0.6823 (tpp) REVERT: D 323 ARG cc_start: 0.8383 (ttm110) cc_final: 0.8060 (ttm-80) REVERT: E 16 LEU cc_start: 0.8519 (tp) cc_final: 0.8262 (tp) REVERT: E 28 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7208 (mt-10) REVERT: E 56 ASN cc_start: 0.8558 (m-40) cc_final: 0.7887 (p0) REVERT: E 74 MET cc_start: 0.7061 (mmp) cc_final: 0.6657 (mmp) REVERT: E 88 LYS cc_start: 0.8041 (mmmm) cc_final: 0.7783 (ttmm) REVERT: E 92 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7674 (t80) REVERT: E 97 MET cc_start: 0.5710 (mmt) cc_final: 0.5058 (mmt) REVERT: E 106 LYS cc_start: 0.8349 (mttm) cc_final: 0.8136 (mttm) REVERT: E 123 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6562 (mmp80) REVERT: E 141 PHE cc_start: 0.7247 (t80) cc_final: 0.6791 (t80) REVERT: F 44 TYR cc_start: 0.7875 (t80) cc_final: 0.7556 (t80) REVERT: F 59 TYR cc_start: 0.7142 (t80) cc_final: 0.6765 (t80) REVERT: F 62 LYS cc_start: 0.8122 (pttm) cc_final: 0.7881 (pttm) REVERT: F 67 TYR cc_start: 0.7564 (t80) cc_final: 0.6570 (t80) REVERT: F 133 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8594 (t) REVERT: F 142 VAL cc_start: 0.8774 (t) cc_final: 0.8020 (m) REVERT: F 147 GLU cc_start: 0.7361 (tt0) cc_final: 0.6869 (tt0) REVERT: F 156 ASN cc_start: 0.8321 (p0) cc_final: 0.7980 (p0) REVERT: F 164 MET cc_start: 0.7056 (ttm) cc_final: 0.6800 (mtm) REVERT: G 251 ILE cc_start: 0.8184 (tt) cc_final: 0.7855 (tp) REVERT: G 257 ASP cc_start: 0.8039 (t70) cc_final: 0.7575 (t70) REVERT: G 276 MET cc_start: 0.6984 (mmm) cc_final: 0.6588 (mmm) REVERT: G 281 GLU cc_start: 0.8171 (pt0) cc_final: 0.7559 (pp20) REVERT: G 284 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7227 (mm-30) REVERT: G 316 GLU cc_start: 0.8251 (tt0) cc_final: 0.8034 (tt0) REVERT: G 322 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7942 (mm-30) REVERT: G 332 GLU cc_start: 0.8218 (tp30) cc_final: 0.7876 (tp30) REVERT: G 345 ASP cc_start: 0.7615 (m-30) cc_final: 0.7306 (m-30) REVERT: G 351 ARG cc_start: 0.7454 (ttp-170) cc_final: 0.6819 (ttp-170) REVERT: G 373 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7461 (mpp80) REVERT: G 428 TYR cc_start: 0.8317 (m-80) cc_final: 0.7474 (m-10) REVERT: G 451 ILE cc_start: 0.8293 (mt) cc_final: 0.7893 (mm) REVERT: G 656 GLU cc_start: 0.7791 (mp0) cc_final: 0.7499 (pm20) REVERT: G 688 GLN cc_start: 0.8536 (tp-100) cc_final: 0.7591 (tp40) REVERT: G 692 MET cc_start: 0.7524 (mmp) cc_final: 0.7161 (mmp) REVERT: H 39 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: H 145 ASP cc_start: 0.7858 (t0) cc_final: 0.7543 (t0) REVERT: I 116 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7217 (mt-10) REVERT: I 122 ARG cc_start: 0.8081 (mpp80) cc_final: 0.6447 (mtt90) REVERT: I 125 GLN cc_start: 0.8399 (tp40) cc_final: 0.8061 (mm-40) REVERT: I 136 LYS cc_start: 0.8218 (mttt) cc_final: 0.7981 (mttt) REVERT: I 142 VAL cc_start: 0.8833 (t) cc_final: 0.8428 (p) REVERT: I 147 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6793 (mm-30) REVERT: I 153 ILE cc_start: 0.8806 (mp) cc_final: 0.8230 (mt) REVERT: I 158 ARG cc_start: 0.8235 (ttm110) cc_final: 0.7716 (ttm110) REVERT: J 216 TYR cc_start: 0.8422 (t80) cc_final: 0.8045 (t80) REVERT: J 237 THR cc_start: 0.8725 (m) cc_final: 0.8503 (p) REVERT: J 256 GLN cc_start: 0.8340 (mt0) cc_final: 0.8110 (mm-40) REVERT: J 259 LYS cc_start: 0.9040 (mmtp) cc_final: 0.8812 (mmtm) REVERT: J 260 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7381 (tmm) REVERT: J 322 GLU cc_start: 0.7970 (tp30) cc_final: 0.7446 (mp0) REVERT: J 438 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.8229 (mtt-85) REVERT: J 458 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8913 (ttpp) REVERT: J 503 GLN cc_start: 0.7479 (tm-30) cc_final: 0.6587 (pp30) REVERT: J 641 LYS cc_start: 0.8080 (pttt) cc_final: 0.7752 (pttm) REVERT: J 679 MET cc_start: 0.6367 (ppp) cc_final: 0.6013 (tmm) REVERT: c 24 ARG cc_start: 0.8220 (mmt-90) cc_final: 0.7976 (tpp-160) REVERT: c 29 LEU cc_start: 0.8436 (mt) cc_final: 0.8233 (mm) REVERT: c 45 LEU cc_start: 0.8082 (mp) cc_final: 0.7842 (mt) REVERT: c 96 ILE cc_start: 0.8770 (pt) cc_final: 0.8392 (pt) REVERT: c 136 GLU cc_start: 0.7903 (tp30) cc_final: 0.7688 (tp30) REVERT: c 142 SER cc_start: 0.8554 (m) cc_final: 0.7979 (p) REVERT: c 170 ASN cc_start: 0.7601 (t0) cc_final: 0.7363 (t0) REVERT: c 183 LYS cc_start: 0.8321 (mtmm) cc_final: 0.8096 (mtpp) REVERT: c 191 ARG cc_start: 0.7486 (mtp180) cc_final: 0.7161 (mtp180) REVERT: c 248 THR cc_start: 0.8703 (m) cc_final: 0.8497 (t) REVERT: c 258 TYR cc_start: 0.8542 (p90) cc_final: 0.8246 (p90) REVERT: c 262 TYR cc_start: 0.8926 (t80) cc_final: 0.8207 (t80) REVERT: c 270 MET cc_start: 0.7517 (ppp) cc_final: 0.7124 (ppp) REVERT: c 271 ASP cc_start: 0.7957 (m-30) cc_final: 0.7119 (m-30) REVERT: C 7 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.6694 (tppt) REVERT: K 142 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7925 (mtp85) REVERT: K 153 PHE cc_start: 0.8310 (m-80) cc_final: 0.7985 (m-80) REVERT: K 183 ASP cc_start: 0.6444 (t0) cc_final: 0.6001 (t0) REVERT: K 258 ASN cc_start: 0.8699 (t0) cc_final: 0.8390 (t0) REVERT: L 292 LEU cc_start: 0.8978 (mm) cc_final: 0.8480 (mm) REVERT: L 294 TRP cc_start: 0.7693 (t60) cc_final: 0.6947 (t60) REVERT: L 297 ASN cc_start: 0.8527 (m110) cc_final: 0.8205 (m110) REVERT: L 301 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8516 (mtmm) REVERT: L 307 MET cc_start: 0.7571 (tpp) cc_final: 0.7224 (tpp) REVERT: L 310 ARG cc_start: 0.7989 (mtp180) cc_final: 0.7637 (mmm-85) REVERT: M 88 LYS cc_start: 0.7919 (mmmm) cc_final: 0.7536 (tppp) REVERT: M 95 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7937 (mt-10) REVERT: M 158 LYS cc_start: 0.8415 (mttt) cc_final: 0.8016 (mttt) REVERT: N 91 GLU cc_start: 0.7201 (mp0) cc_final: 0.6934 (mp0) REVERT: N 98 GLN cc_start: 0.8350 (mt0) cc_final: 0.7844 (mt0) REVERT: N 136 LYS cc_start: 0.8589 (mttt) cc_final: 0.8317 (mtpp) REVERT: N 185 GLU cc_start: 0.7480 (tt0) cc_final: 0.6879 (tt0) REVERT: O 281 GLU cc_start: 0.8556 (pt0) cc_final: 0.7907 (pp20) REVERT: O 284 GLU cc_start: 0.7972 (tp30) cc_final: 0.7464 (tp30) REVERT: O 286 GLN cc_start: 0.8969 (mt0) cc_final: 0.8766 (mt0) REVERT: O 287 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8791 (mmmt) REVERT: O 331 ASP cc_start: 0.8663 (p0) cc_final: 0.8414 (p0) REVERT: O 347 HIS cc_start: 0.8858 (m170) cc_final: 0.8626 (m170) REVERT: O 350 GLN cc_start: 0.8399 (tm-30) cc_final: 0.7505 (tm-30) REVERT: O 371 GLU cc_start: 0.7089 (tp30) cc_final: 0.6426 (tp30) REVERT: O 438 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7944 (mtp85) REVERT: O 502 TYR cc_start: 0.6194 (p90) cc_final: 0.4731 (p90) REVERT: O 547 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8160 (mt0) REVERT: O 641 LYS cc_start: 0.8284 (mmtt) cc_final: 0.8071 (mmtt) REVERT: O 692 MET cc_start: 0.7838 (mtm) cc_final: 0.7512 (mtm) REVERT: P 33 MET cc_start: 0.8149 (mmt) cc_final: 0.7937 (tpp) REVERT: P 78 ASN cc_start: 0.7406 (t0) cc_final: 0.6957 (t0) REVERT: P 94 MET cc_start: 0.7472 (mmp) cc_final: 0.7240 (mmp) REVERT: P 180 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7748 (mt-10) REVERT: P 250 TYR cc_start: 0.6031 (t80) cc_final: 0.5753 (t80) REVERT: P 267 GLU cc_start: 0.6922 (mp0) cc_final: 0.6025 (mp0) REVERT: Q 116 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7003 (mt-10) REVERT: Q 121 GLN cc_start: 0.6169 (mp10) cc_final: 0.5675 (mp10) REVERT: Q 151 GLU cc_start: 0.6936 (tp30) cc_final: 0.6439 (tp30) REVERT: Q 156 ASN cc_start: 0.8352 (m110) cc_final: 0.7584 (m-40) REVERT: Q 173 LYS cc_start: 0.8456 (ptpp) cc_final: 0.7973 (ptpp) REVERT: Q 181 GLU cc_start: 0.7634 (tt0) cc_final: 0.7324 (tt0) REVERT: R 207 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.6566 (pp20) REVERT: R 211 GLN cc_start: 0.8089 (mt0) cc_final: 0.7835 (mm-40) REVERT: R 212 ASN cc_start: 0.7545 (t0) cc_final: 0.7201 (t0) REVERT: R 249 ASP cc_start: 0.8419 (t0) cc_final: 0.8167 (t0) REVERT: R 260 MET cc_start: 0.7872 (tpp) cc_final: 0.7463 (tpp) REVERT: R 284 GLU cc_start: 0.7566 (tp30) cc_final: 0.7135 (tp30) REVERT: R 313 ASN cc_start: 0.8329 (t0) cc_final: 0.7632 (t0) REVERT: R 316 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7919 (tm-30) REVERT: R 322 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7541 (tm-30) REVERT: R 334 TYR cc_start: 0.8102 (t80) cc_final: 0.7850 (t80) REVERT: R 433 CYS cc_start: 0.7616 (p) cc_final: 0.7302 (p) REVERT: R 464 ARG cc_start: 0.7457 (mtm-85) cc_final: 0.7152 (mtm-85) REVERT: R 470 ILE cc_start: 0.8857 (mm) cc_final: 0.8381 (pt) REVERT: R 530 ILE cc_start: 0.8877 (mm) cc_final: 0.8451 (tp) REVERT: R 556 ASN cc_start: 0.8792 (m-40) cc_final: 0.8416 (m-40) REVERT: R 640 LYS cc_start: 0.8684 (tptt) cc_final: 0.8369 (tptm) REVERT: d 25 ARG cc_start: 0.8542 (ttm-80) cc_final: 0.8239 (ttm-80) REVERT: d 28 LEU cc_start: 0.8631 (tp) cc_final: 0.8369 (tt) REVERT: d 38 ASP cc_start: 0.8158 (m-30) cc_final: 0.7848 (m-30) REVERT: d 43 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7751 (ttp80) REVERT: d 81 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6945 (mt-10) REVERT: d 170 ASN cc_start: 0.7685 (t0) cc_final: 0.7092 (t0) REVERT: d 180 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7346 (mm-30) REVERT: d 183 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8388 (ptpp) REVERT: d 230 MET cc_start: 0.7338 (mmm) cc_final: 0.6975 (mmm) REVERT: d 248 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8637 (p) REVERT: d 269 ASN cc_start: 0.8806 (t0) cc_final: 0.8558 (t0) outliers start: 142 outliers final: 99 residues processed: 1208 average time/residue: 0.2396 time to fit residues: 440.4226 Evaluate side-chains 1246 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1135 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 617 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 275 MET Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 133 THR Chi-restraints excluded: chain I residue 157 HIS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain J residue 458 LYS Chi-restraints excluded: chain J residue 587 GLU Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain J residue 598 GLU Chi-restraints excluded: chain c residue 33 MET Chi-restraints excluded: chain c residue 67 GLN Chi-restraints excluded: chain c residue 73 THR Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 174 GLU Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 257 ASN Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 286 LYS Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 314 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain O residue 433 CYS Chi-restraints excluded: chain O residue 540 SER Chi-restraints excluded: chain O residue 547 GLN Chi-restraints excluded: chain O residue 647 ILE Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 81 GLU Chi-restraints excluded: chain P residue 144 ILE Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 227 SER Chi-restraints excluded: chain P residue 271 ASP Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain Q residue 114 THR Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 157 HIS Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 248 VAL Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 456 LYS Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 647 ILE Chi-restraints excluded: chain R residue 677 THR Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Chi-restraints excluded: chain d residue 257 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 174 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 307 optimal weight: 0.0980 chunk 381 optimal weight: 0.5980 chunk 250 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 324 optimal weight: 0.7980 chunk 330 optimal weight: 2.9990 chunk 314 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN G 547 GLN ** G 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 109 HIS c 234 ASN c 257 ASN K 266 HIS M 162 ASN O 531 GLN O 615 ASN ** P 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 157 HIS ** R 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 657 ASN d 18 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.131357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110203 restraints weight = 72821.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.114087 restraints weight = 34940.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116689 restraints weight = 21247.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.118130 restraints weight = 14872.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.119224 restraints weight = 11857.156| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34806 Z= 0.175 Angle : 0.673 13.008 47180 Z= 0.345 Chirality : 0.044 0.194 4964 Planarity : 0.005 0.091 6150 Dihedral : 5.052 44.853 4634 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.87 % Favored : 94.96 % Rotamer: Outliers : 4.09 % Allowed : 20.80 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.13), residues: 4110 helix: 0.30 (0.15), residues: 1140 sheet: -1.04 (0.17), residues: 793 loop : -0.48 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 442 TYR 0.035 0.002 TYR I 44 PHE 0.032 0.001 PHE B 213 TRP 0.031 0.002 TRP M 187 HIS 0.007 0.001 HIS F 157 Details of bonding type rmsd covalent geometry : bond 0.00385 (34806) covalent geometry : angle 0.67306 (47180) hydrogen bonds : bond 0.03951 ( 1325) hydrogen bonds : angle 5.60173 ( 3786) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1322 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 1173 time to evaluate : 1.374 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: 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: symmetry clash REVERT: A 3 THR cc_start: 0.8838 (p) cc_final: 0.8602 (m) REVERT: A 7 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.6449 (mptp) REVERT: A 21 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8482 (p) REVERT: B 150 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7374 (t0) REVERT: B 215 VAL cc_start: 0.8719 (t) cc_final: 0.8436 (m) REVERT: B 226 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7007 (mt-10) REVERT: B 253 ASP cc_start: 0.7867 (t0) cc_final: 0.7645 (t0) REVERT: D 294 TRP cc_start: 0.7736 (t60) cc_final: 0.6268 (t60) REVERT: D 298 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7367 (mm-30) REVERT: D 301 LYS cc_start: 0.8771 (mtmt) cc_final: 0.8306 (mtmt) REVERT: D 307 MET cc_start: 0.7143 (tpp) cc_final: 0.6825 (tpp) REVERT: D 323 ARG cc_start: 0.8400 (ttm110) cc_final: 0.8110 (ttm-80) REVERT: E 28 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7138 (mm-30) REVERT: E 44 ARG cc_start: 0.7546 (ttp-110) cc_final: 0.7193 (ttp-110) REVERT: E 92 TYR cc_start: 0.8322 (OUTLIER) cc_final: 0.7730 (t80) REVERT: E 97 MET cc_start: 0.5715 (mmt) cc_final: 0.5153 (mmt) REVERT: E 106 LYS cc_start: 0.8324 (mttm) cc_final: 0.8121 (mttm) REVERT: E 123 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6689 (mmp80) REVERT: F 44 TYR cc_start: 0.7885 (t80) cc_final: 0.7533 (t80) REVERT: F 59 TYR cc_start: 0.7212 (t80) cc_final: 0.6843 (t80) REVERT: F 62 LYS cc_start: 0.8123 (pttm) cc_final: 0.7915 (pttm) REVERT: F 67 TYR cc_start: 0.7573 (t80) cc_final: 0.6507 (t80) REVERT: F 98 GLN cc_start: 0.8408 (mm-40) cc_final: 0.7386 (mm-40) REVERT: F 122 ARG cc_start: 0.8267 (mpp80) cc_final: 0.7772 (mtt90) REVERT: F 133 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8675 (t) REVERT: F 142 VAL cc_start: 0.8733 (t) cc_final: 0.7933 (m) REVERT: F 147 GLU cc_start: 0.7440 (tt0) cc_final: 0.6857 (tt0) REVERT: F 156 ASN cc_start: 0.8311 (p0) cc_final: 0.7980 (p0) REVERT: G 251 ILE cc_start: 0.8174 (tt) cc_final: 0.7858 (tp) REVERT: G 257 ASP cc_start: 0.8033 (t70) cc_final: 0.7566 (t70) REVERT: G 276 MET cc_start: 0.6959 (mmm) cc_final: 0.6557 (mmm) REVERT: G 281 GLU cc_start: 0.8163 (pt0) cc_final: 0.7554 (pp20) REVERT: G 284 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7209 (mm-30) REVERT: G 316 GLU cc_start: 0.8244 (tt0) cc_final: 0.7906 (tt0) REVERT: G 332 GLU cc_start: 0.8203 (tp30) cc_final: 0.7863 (tp30) REVERT: G 345 ASP cc_start: 0.7646 (m-30) cc_final: 0.7320 (m-30) REVERT: G 351 ARG cc_start: 0.7423 (ttp-170) cc_final: 0.6934 (ttp-170) REVERT: G 428 TYR cc_start: 0.8358 (m-80) cc_final: 0.7376 (m-10) REVERT: G 451 ILE cc_start: 0.8320 (mt) cc_final: 0.7932 (mm) REVERT: G 656 GLU cc_start: 0.7781 (mp0) cc_final: 0.7515 (pm20) REVERT: G 688 GLN cc_start: 0.8644 (tp-100) cc_final: 0.7749 (tp40) REVERT: G 692 MET cc_start: 0.7522 (mmp) cc_final: 0.7206 (mmp) REVERT: H 39 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: H 110 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7440 (mm-30) REVERT: H 145 ASP cc_start: 0.7899 (t0) cc_final: 0.7563 (t0) REVERT: H 269 ASN cc_start: 0.8546 (t0) cc_final: 0.8343 (t0) REVERT: I 116 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7190 (mt-10) REVERT: I 125 GLN cc_start: 0.8404 (tp40) cc_final: 0.8102 (mm-40) REVERT: I 136 LYS cc_start: 0.8220 (mttt) cc_final: 0.7994 (mttt) REVERT: I 142 VAL cc_start: 0.8850 (t) cc_final: 0.8461 (p) REVERT: I 153 ILE cc_start: 0.8831 (mp) cc_final: 0.8242 (mt) REVERT: I 158 ARG cc_start: 0.8229 (ttm110) cc_final: 0.7643 (ttm110) REVERT: I 185 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7350 (mt-10) REVERT: J 211 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7856 (mm-40) REVERT: J 216 TYR cc_start: 0.8422 (t80) cc_final: 0.8064 (t80) REVERT: J 237 THR cc_start: 0.8717 (m) cc_final: 0.8507 (p) REVERT: J 256 GLN cc_start: 0.8352 (mt0) cc_final: 0.8057 (mm110) REVERT: J 260 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7341 (tmm) REVERT: J 276 MET cc_start: 0.6678 (tmm) cc_final: 0.6340 (tmm) REVERT: J 281 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7195 (mp0) REVERT: J 322 GLU cc_start: 0.7962 (tp30) cc_final: 0.7397 (mp0) REVERT: J 587 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7242 (pt0) REVERT: c 24 ARG cc_start: 0.8204 (mmt-90) cc_final: 0.7708 (tpp80) REVERT: c 45 LEU cc_start: 0.8104 (mp) cc_final: 0.7861 (mt) REVERT: c 96 ILE cc_start: 0.8744 (pt) cc_final: 0.8342 (pt) REVERT: c 136 GLU cc_start: 0.7902 (tp30) cc_final: 0.7699 (tp30) REVERT: c 142 SER cc_start: 0.8532 (m) cc_final: 0.8008 (p) REVERT: c 170 ASN cc_start: 0.7638 (t0) cc_final: 0.7367 (t0) REVERT: c 191 ARG cc_start: 0.7514 (mtp180) cc_final: 0.7219 (mtp180) REVERT: c 248 THR cc_start: 0.8699 (m) cc_final: 0.8488 (t) REVERT: c 258 TYR cc_start: 0.8332 (p90) cc_final: 0.7909 (p90) REVERT: c 262 TYR cc_start: 0.8890 (t80) cc_final: 0.8205 (t80) REVERT: c 269 ASN cc_start: 0.8229 (t0) cc_final: 0.7867 (t0) REVERT: c 270 MET cc_start: 0.7589 (ppp) cc_final: 0.7181 (ppp) REVERT: c 271 ASP cc_start: 0.7831 (m-30) cc_final: 0.6965 (m-30) REVERT: C 7 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.6556 (tppt) REVERT: K 153 PHE cc_start: 0.8255 (m-80) cc_final: 0.7896 (m-80) REVERT: K 183 ASP cc_start: 0.6379 (t0) cc_final: 0.5924 (t0) REVERT: K 253 ASP cc_start: 0.7719 (m-30) cc_final: 0.7218 (t0) REVERT: K 287 LYS cc_start: 0.8394 (mtpt) cc_final: 0.7995 (mttp) REVERT: L 294 TRP cc_start: 0.7753 (t60) cc_final: 0.6778 (t60) REVERT: L 298 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7674 (mm-30) REVERT: M 88 LYS cc_start: 0.8014 (mmmm) cc_final: 0.7617 (tppp) REVERT: M 92 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7634 (t80) REVERT: M 96 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8429 (mm) REVERT: M 158 LYS cc_start: 0.8391 (mttt) cc_final: 0.8024 (mttt) REVERT: M 193 MET cc_start: 0.7552 (mmm) cc_final: 0.6964 (tmm) REVERT: N 91 GLU cc_start: 0.7203 (mp0) cc_final: 0.6922 (mp0) REVERT: N 98 GLN cc_start: 0.8342 (mt0) cc_final: 0.7837 (mt0) REVERT: N 116 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7081 (mm-30) REVERT: N 136 LYS cc_start: 0.8584 (mttt) cc_final: 0.8323 (mtpp) REVERT: N 182 GLN cc_start: 0.8016 (tp40) cc_final: 0.7225 (tm-30) REVERT: N 185 GLU cc_start: 0.7491 (tt0) cc_final: 0.6986 (tt0) REVERT: N 195 GLU cc_start: 0.4442 (mt-10) cc_final: 0.4141 (mm-30) REVERT: O 281 GLU cc_start: 0.8540 (pt0) cc_final: 0.7948 (pp20) REVERT: O 286 GLN cc_start: 0.8982 (mt0) cc_final: 0.8762 (mt0) REVERT: O 287 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8723 (mmmt) REVERT: O 331 ASP cc_start: 0.8683 (p0) cc_final: 0.8442 (p0) REVERT: O 347 HIS cc_start: 0.8843 (m170) cc_final: 0.8628 (m170) REVERT: O 350 GLN cc_start: 0.8396 (tm-30) cc_final: 0.7502 (tm-30) REVERT: O 371 GLU cc_start: 0.7104 (tp30) cc_final: 0.6410 (tp30) REVERT: O 438 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7903 (mtp85) REVERT: O 502 TYR cc_start: 0.6234 (p90) cc_final: 0.4811 (p90) REVERT: O 547 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8160 (mt0) REVERT: O 641 LYS cc_start: 0.8303 (mmtt) cc_final: 0.8049 (mmtt) REVERT: P 28 LEU cc_start: 0.8592 (tp) cc_final: 0.8023 (mm) REVERT: P 43 ARG cc_start: 0.7945 (mtm-85) cc_final: 0.7212 (mtm-85) REVERT: P 94 MET cc_start: 0.7459 (mmp) cc_final: 0.7148 (mmp) REVERT: P 180 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7746 (mt-10) REVERT: P 267 GLU cc_start: 0.6967 (mp0) cc_final: 0.6045 (mp0) REVERT: Q 106 TYR cc_start: 0.8020 (m-80) cc_final: 0.7450 (m-80) REVERT: Q 116 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7029 (mt-10) REVERT: Q 121 GLN cc_start: 0.6297 (mp10) cc_final: 0.5804 (mp10) REVERT: Q 156 ASN cc_start: 0.8295 (m110) cc_final: 0.7653 (m-40) REVERT: Q 173 LYS cc_start: 0.8502 (ptpp) cc_final: 0.7864 (ptpp) REVERT: Q 181 GLU cc_start: 0.7670 (tt0) cc_final: 0.7229 (tt0) REVERT: R 207 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: R 249 ASP cc_start: 0.8407 (t0) cc_final: 0.8173 (t0) REVERT: R 260 MET cc_start: 0.7844 (tpp) cc_final: 0.7407 (tpp) REVERT: R 313 ASN cc_start: 0.8298 (t0) cc_final: 0.7649 (t0) REVERT: R 316 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7896 (tm-30) REVERT: R 322 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7499 (tm-30) REVERT: R 334 TYR cc_start: 0.8086 (t80) cc_final: 0.7739 (t80) REVERT: R 371 GLU cc_start: 0.7515 (tm-30) cc_final: 0.6928 (tm-30) REVERT: R 433 CYS cc_start: 0.7699 (p) cc_final: 0.7380 (p) REVERT: R 464 ARG cc_start: 0.7482 (mtm-85) cc_final: 0.7189 (mtm-85) REVERT: R 470 ILE cc_start: 0.8853 (mm) cc_final: 0.8421 (pt) REVERT: R 503 GLN cc_start: 0.7591 (pm20) cc_final: 0.6418 (pm20) REVERT: R 522 GLU cc_start: 0.7403 (pm20) cc_final: 0.6760 (pm20) REVERT: R 523 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7439 (mm-30) REVERT: R 530 ILE cc_start: 0.8854 (mm) cc_final: 0.8435 (tp) REVERT: R 556 ASN cc_start: 0.8802 (m-40) cc_final: 0.8434 (m-40) REVERT: R 619 GLN cc_start: 0.8016 (tp40) cc_final: 0.7631 (tp-100) REVERT: R 640 LYS cc_start: 0.8683 (tptt) cc_final: 0.8377 (tptm) REVERT: R 679 MET cc_start: 0.4328 (tmm) cc_final: 0.3889 (tmm) REVERT: d 25 ARG cc_start: 0.8506 (ttm-80) cc_final: 0.8292 (ttm-80) REVERT: d 28 LEU cc_start: 0.8645 (tp) cc_final: 0.8394 (tt) REVERT: d 38 ASP cc_start: 0.8115 (m-30) cc_final: 0.7848 (m-30) REVERT: d 43 ARG cc_start: 0.8230 (ttp80) cc_final: 0.7690 (ttp80) REVERT: d 49 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7952 (ttp80) REVERT: d 56 ASP cc_start: 0.8444 (m-30) cc_final: 0.7912 (m-30) REVERT: d 81 GLU cc_start: 0.7550 (mt-10) cc_final: 0.6982 (mt-10) REVERT: d 170 ASN cc_start: 0.7725 (t0) cc_final: 0.7098 (t0) REVERT: d 180 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7310 (mm-30) REVERT: d 183 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8394 (ptpp) REVERT: d 248 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8607 (p) REVERT: d 269 ASN cc_start: 0.8833 (t0) cc_final: 0.8551 (t0) outliers start: 149 outliers final: 109 residues processed: 1224 average time/residue: 0.2499 time to fit residues: 464.8732 Evaluate side-chains 1261 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 1137 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 453 THR Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 617 ILE Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 159 LEU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 267 GLU Chi-restraints excluded: chain H residue 275 MET Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 157 HIS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain J residue 587 GLU Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain J residue 598 GLU Chi-restraints excluded: chain c residue 33 MET Chi-restraints excluded: chain c residue 67 GLN Chi-restraints excluded: chain c residue 73 THR Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain c residue 174 GLU Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 291 PHE Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 13 GLU Chi-restraints excluded: chain M residue 65 MET Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 135 SER Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 314 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain O residue 433 CYS Chi-restraints excluded: chain O residue 435 VAL Chi-restraints excluded: chain O residue 446 VAL Chi-restraints excluded: chain O residue 540 SER Chi-restraints excluded: chain O residue 547 GLN Chi-restraints excluded: chain O residue 615 ASN Chi-restraints excluded: chain O residue 647 ILE Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 227 SER Chi-restraints excluded: chain P residue 248 THR Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 271 ASP Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain Q residue 114 THR Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 157 HIS Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 616 LEU Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 647 ILE Chi-restraints excluded: chain R residue 677 THR Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Chi-restraints excluded: chain d residue 254 ARG Chi-restraints excluded: chain d residue 257 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 128 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 338 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 234 optimal weight: 0.0670 chunk 341 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 294 optimal weight: 0.0050 chunk 219 optimal weight: 0.8980 chunk 306 optimal weight: 4.9990 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 544 HIS G 547 GLN ** G 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 HIS J 323 GLN J 350 GLN c 109 HIS c 234 ASN N 31 HIS O 323 GLN ** O 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 229 GLN d 257 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.131724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.110601 restraints weight = 72424.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.114486 restraints weight = 34742.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.117030 restraints weight = 21143.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.118708 restraints weight = 14892.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.119680 restraints weight = 11566.149| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34806 Z= 0.157 Angle : 0.669 13.080 47180 Z= 0.344 Chirality : 0.044 0.191 4964 Planarity : 0.005 0.076 6150 Dihedral : 5.000 44.006 4634 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.94 % Favored : 94.91 % Rotamer: Outliers : 4.12 % Allowed : 21.49 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.13), residues: 4110 helix: 0.33 (0.15), residues: 1142 sheet: -1.06 (0.18), residues: 785 loop : -0.43 (0.14), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 232 TYR 0.025 0.002 TYR R 667 PHE 0.030 0.001 PHE B 213 TRP 0.019 0.001 TRP M 187 HIS 0.007 0.001 HIS F 157 Details of bonding type rmsd covalent geometry : bond 0.00351 (34806) covalent geometry : angle 0.66932 (47180) hydrogen bonds : bond 0.03846 ( 1325) hydrogen bonds : angle 5.55514 ( 3786) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 1160 time to evaluate : 1.377 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: 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: A 7 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.6344 (tptp) REVERT: A 20 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7186 (tm-30) REVERT: B 150 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7308 (t0) REVERT: B 215 VAL cc_start: 0.8743 (t) cc_final: 0.8484 (m) REVERT: B 218 LYS cc_start: 0.7876 (mttp) cc_final: 0.7642 (mttp) REVERT: B 226 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7032 (mt-10) REVERT: B 253 ASP cc_start: 0.7837 (t0) cc_final: 0.7548 (t0) REVERT: D 294 TRP cc_start: 0.7742 (t60) cc_final: 0.6313 (t60) REVERT: D 298 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7366 (mm-30) REVERT: D 301 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8305 (mtmt) REVERT: D 307 MET cc_start: 0.7151 (tpp) cc_final: 0.6775 (tpp) REVERT: D 323 ARG cc_start: 0.8399 (ttm110) cc_final: 0.8092 (ttm-80) REVERT: E 44 ARG cc_start: 0.7560 (ttp-110) cc_final: 0.7231 (ttp-110) REVERT: E 46 LYS cc_start: 0.7561 (tttm) cc_final: 0.7106 (tmtm) REVERT: E 74 MET cc_start: 0.6919 (mmp) cc_final: 0.6035 (mmm) REVERT: E 97 MET cc_start: 0.5711 (mmt) cc_final: 0.5027 (mmt) REVERT: E 106 LYS cc_start: 0.8338 (mttm) cc_final: 0.8130 (mttm) REVERT: E 123 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.6344 (mmp80) REVERT: E 175 GLU cc_start: 0.7210 (pp20) cc_final: 0.6871 (pp20) REVERT: F 44 TYR cc_start: 0.7890 (t80) cc_final: 0.7545 (t80) REVERT: F 59 TYR cc_start: 0.7204 (t80) cc_final: 0.6864 (t80) REVERT: F 62 LYS cc_start: 0.8110 (pttm) cc_final: 0.7904 (pttm) REVERT: F 67 TYR cc_start: 0.7544 (t80) cc_final: 0.6496 (t80) REVERT: F 98 GLN cc_start: 0.8341 (mm-40) cc_final: 0.7307 (mm-40) REVERT: F 116 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6767 (mt-10) REVERT: F 122 ARG cc_start: 0.8213 (mpp80) cc_final: 0.7710 (mtt90) REVERT: F 133 THR cc_start: 0.8941 (OUTLIER) cc_final: 0.8712 (t) REVERT: F 142 VAL cc_start: 0.8723 (t) cc_final: 0.7867 (m) REVERT: F 147 GLU cc_start: 0.7373 (tt0) cc_final: 0.6834 (tt0) REVERT: F 156 ASN cc_start: 0.8315 (p0) cc_final: 0.8001 (p0) REVERT: G 210 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7470 (tp) REVERT: G 251 ILE cc_start: 0.8180 (tt) cc_final: 0.7859 (tp) REVERT: G 257 ASP cc_start: 0.8030 (t70) cc_final: 0.7554 (t70) REVERT: G 276 MET cc_start: 0.6983 (mmm) cc_final: 0.6557 (mmm) REVERT: G 281 GLU cc_start: 0.8153 (pt0) cc_final: 0.7541 (pp20) REVERT: G 284 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7164 (mm-30) REVERT: G 316 GLU cc_start: 0.8216 (tt0) cc_final: 0.7758 (tt0) REVERT: G 322 GLU cc_start: 0.8193 (tp30) cc_final: 0.7919 (mm-30) REVERT: G 332 GLU cc_start: 0.8209 (tp30) cc_final: 0.7877 (tp30) REVERT: G 345 ASP cc_start: 0.7638 (m-30) cc_final: 0.7281 (m-30) REVERT: G 351 ARG cc_start: 0.7415 (ttp-170) cc_final: 0.6978 (ttp-170) REVERT: G 428 TYR cc_start: 0.8344 (m-80) cc_final: 0.7328 (m-10) REVERT: G 451 ILE cc_start: 0.8313 (mt) cc_final: 0.7920 (mm) REVERT: G 592 LEU cc_start: 0.8268 (mm) cc_final: 0.7964 (tp) REVERT: G 611 GLN cc_start: 0.8364 (pt0) cc_final: 0.8154 (pt0) REVERT: G 656 GLU cc_start: 0.7776 (mp0) cc_final: 0.7548 (pm20) REVERT: G 688 GLN cc_start: 0.8649 (tp-100) cc_final: 0.7658 (tp40) REVERT: G 692 MET cc_start: 0.7551 (mmp) cc_final: 0.7246 (mmp) REVERT: H 39 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: H 110 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7394 (mm-30) REVERT: H 145 ASP cc_start: 0.7932 (t0) cc_final: 0.7583 (t0) REVERT: H 171 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7932 (ptm-80) REVERT: I 66 ARG cc_start: 0.7772 (ttm-80) cc_final: 0.7443 (ttm-80) REVERT: I 111 ASP cc_start: 0.7973 (m-30) cc_final: 0.7702 (m-30) REVERT: I 116 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7163 (mt-10) REVERT: I 125 GLN cc_start: 0.8412 (tp40) cc_final: 0.8099 (mm-40) REVERT: I 136 LYS cc_start: 0.8227 (mttt) cc_final: 0.7957 (mttt) REVERT: I 142 VAL cc_start: 0.8723 (t) cc_final: 0.8472 (p) REVERT: I 153 ILE cc_start: 0.8823 (mp) cc_final: 0.8203 (mt) REVERT: I 158 ARG cc_start: 0.8225 (ttm110) cc_final: 0.7605 (ttm110) REVERT: I 185 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7302 (mt-10) REVERT: J 211 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7838 (mm-40) REVERT: J 216 TYR cc_start: 0.8456 (t80) cc_final: 0.8055 (t80) REVERT: J 218 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7815 (tt) REVERT: J 237 THR cc_start: 0.8713 (m) cc_final: 0.8505 (p) REVERT: J 260 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7277 (tmm) REVERT: J 322 GLU cc_start: 0.7957 (tp30) cc_final: 0.7391 (mp0) REVERT: J 619 GLN cc_start: 0.7215 (pm20) cc_final: 0.6888 (pm20) REVERT: J 640 LYS cc_start: 0.8563 (tptp) cc_final: 0.8351 (tptm) REVERT: c 24 ARG cc_start: 0.8200 (mmt-90) cc_final: 0.7721 (tpp80) REVERT: c 45 LEU cc_start: 0.8108 (mp) cc_final: 0.7861 (mt) REVERT: c 56 ASP cc_start: 0.8178 (m-30) cc_final: 0.7965 (m-30) REVERT: c 96 ILE cc_start: 0.8743 (pt) cc_final: 0.8318 (pt) REVERT: c 142 SER cc_start: 0.8513 (m) cc_final: 0.8075 (p) REVERT: c 170 ASN cc_start: 0.7603 (t0) cc_final: 0.7319 (t0) REVERT: c 191 ARG cc_start: 0.7540 (mtp180) cc_final: 0.7219 (mtp180) REVERT: c 258 TYR cc_start: 0.8336 (p90) cc_final: 0.7938 (p90) REVERT: c 262 TYR cc_start: 0.8858 (t80) cc_final: 0.8220 (t80) REVERT: c 269 ASN cc_start: 0.8364 (t0) cc_final: 0.7936 (t0) REVERT: c 270 MET cc_start: 0.7595 (ppp) cc_final: 0.7177 (ppp) REVERT: c 271 ASP cc_start: 0.7790 (m-30) cc_final: 0.6865 (m-30) REVERT: C 7 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.6697 (tptt) REVERT: K 142 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7621 (ttp80) REVERT: K 153 PHE cc_start: 0.8237 (m-80) cc_final: 0.7866 (m-80) REVERT: K 183 ASP cc_start: 0.6401 (t0) cc_final: 0.5919 (t0) REVERT: K 253 ASP cc_start: 0.7743 (m-30) cc_final: 0.7194 (t0) REVERT: K 287 LYS cc_start: 0.8390 (mtpt) cc_final: 0.7989 (mttp) REVERT: L 294 TRP cc_start: 0.7761 (t60) cc_final: 0.6751 (t60) REVERT: L 298 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7690 (mm-30) REVERT: L 307 MET cc_start: 0.7492 (tpp) cc_final: 0.7179 (tpp) REVERT: M 97 MET cc_start: 0.6002 (mmt) cc_final: 0.5637 (mmt) REVERT: M 158 LYS cc_start: 0.8377 (mttt) cc_final: 0.8006 (mttt) REVERT: M 191 TRP cc_start: 0.8179 (t-100) cc_final: 0.7890 (t-100) REVERT: M 193 MET cc_start: 0.7532 (mmm) cc_final: 0.6993 (tmm) REVERT: N 91 GLU cc_start: 0.7170 (mp0) cc_final: 0.6887 (mp0) REVERT: N 98 GLN cc_start: 0.8309 (mt0) cc_final: 0.7803 (mt0) REVERT: N 116 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7071 (mm-30) REVERT: N 136 LYS cc_start: 0.8579 (mttt) cc_final: 0.8316 (mtpp) REVERT: N 185 GLU cc_start: 0.7501 (tt0) cc_final: 0.7001 (tt0) REVERT: O 281 GLU cc_start: 0.8528 (pt0) cc_final: 0.7924 (pp20) REVERT: O 284 GLU cc_start: 0.7954 (tp30) cc_final: 0.7370 (tp30) REVERT: O 287 LYS cc_start: 0.8915 (mmmt) cc_final: 0.8605 (mmmt) REVERT: O 347 HIS cc_start: 0.8840 (m170) cc_final: 0.8630 (m170) REVERT: O 350 GLN cc_start: 0.8405 (tm-30) cc_final: 0.7559 (tm-30) REVERT: O 371 GLU cc_start: 0.7105 (tp30) cc_final: 0.6460 (tp30) REVERT: O 438 ARG cc_start: 0.8159 (ttm-80) cc_final: 0.7888 (mtp85) REVERT: O 502 TYR cc_start: 0.6237 (p90) cc_final: 0.4832 (p90) REVERT: O 524 ASN cc_start: 0.8525 (t0) cc_final: 0.8247 (t0) REVERT: O 547 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8155 (mt0) REVERT: O 636 PHE cc_start: 0.7770 (m-80) cc_final: 0.7509 (m-80) REVERT: O 685 GLU cc_start: 0.8268 (mp0) cc_final: 0.7942 (mp0) REVERT: O 688 GLN cc_start: 0.8521 (tm-30) cc_final: 0.7841 (tm-30) REVERT: O 692 MET cc_start: 0.7768 (mtm) cc_final: 0.7129 (mtm) REVERT: P 43 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7215 (mtm-85) REVERT: P 94 MET cc_start: 0.7429 (mmp) cc_final: 0.7134 (mmp) REVERT: P 180 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7728 (mt-10) REVERT: P 267 GLU cc_start: 0.6976 (mp0) cc_final: 0.6133 (mp0) REVERT: Q 116 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7025 (mt-10) REVERT: Q 121 GLN cc_start: 0.6292 (mp10) cc_final: 0.5746 (mp10) REVERT: Q 122 ARG cc_start: 0.8070 (mpp80) cc_final: 0.7777 (mpp80) REVERT: Q 151 GLU cc_start: 0.7578 (tp30) cc_final: 0.5987 (tp30) REVERT: Q 156 ASN cc_start: 0.8131 (m110) cc_final: 0.7606 (m-40) REVERT: Q 158 ARG cc_start: 0.7227 (mtt-85) cc_final: 0.6994 (ttm110) REVERT: Q 160 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.7005 (mm-40) REVERT: Q 173 LYS cc_start: 0.8509 (ptpp) cc_final: 0.7812 (ptpp) REVERT: Q 181 GLU cc_start: 0.7658 (tt0) cc_final: 0.7198 (tt0) REVERT: R 205 MET cc_start: 0.5129 (tpt) cc_final: 0.3961 (tpt) REVERT: R 207 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.6165 (mp0) REVERT: R 212 ASN cc_start: 0.7485 (t0) cc_final: 0.7203 (t0) REVERT: R 260 MET cc_start: 0.7831 (tpp) cc_final: 0.7516 (tpp) REVERT: R 313 ASN cc_start: 0.8274 (t0) cc_final: 0.7635 (t0) REVERT: R 316 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7941 (tm-30) REVERT: R 322 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7525 (tm-30) REVERT: R 334 TYR cc_start: 0.8228 (t80) cc_final: 0.7846 (t80) REVERT: R 335 ARG cc_start: 0.8415 (mmt90) cc_final: 0.8202 (mtt-85) REVERT: R 373 ARG cc_start: 0.6854 (ptp90) cc_final: 0.6396 (ptp90) REVERT: R 433 CYS cc_start: 0.7705 (p) cc_final: 0.7391 (p) REVERT: R 464 ARG cc_start: 0.7514 (mtm-85) cc_final: 0.7021 (mtm-85) REVERT: R 470 ILE cc_start: 0.8849 (mm) cc_final: 0.8447 (pt) REVERT: R 530 ILE cc_start: 0.8839 (mm) cc_final: 0.8453 (tp) REVERT: R 556 ASN cc_start: 0.8803 (m-40) cc_final: 0.8419 (m-40) REVERT: R 640 LYS cc_start: 0.8670 (tptt) cc_final: 0.8358 (tptm) REVERT: R 679 MET cc_start: 0.4339 (OUTLIER) cc_final: 0.3922 (tmm) REVERT: d 25 ARG cc_start: 0.8509 (ttm-80) cc_final: 0.8278 (ttm-80) REVERT: d 28 LEU cc_start: 0.8625 (tp) cc_final: 0.8396 (tt) REVERT: d 33 MET cc_start: 0.7872 (tpp) cc_final: 0.7610 (tpp) REVERT: d 38 ASP cc_start: 0.8117 (m-30) cc_final: 0.7848 (m-30) REVERT: d 43 ARG cc_start: 0.8209 (ttp80) cc_final: 0.7655 (ttp80) REVERT: d 56 ASP cc_start: 0.8428 (m-30) cc_final: 0.8110 (m-30) REVERT: d 81 GLU cc_start: 0.7558 (mt-10) cc_final: 0.6980 (mt-10) REVERT: d 102 ARG cc_start: 0.7839 (mtp85) cc_final: 0.6967 (mtp85) REVERT: d 170 ASN cc_start: 0.7744 (t0) cc_final: 0.7120 (t0) REVERT: d 180 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7292 (mm-30) REVERT: d 183 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8403 (ptpp) REVERT: d 220 ASP cc_start: 0.7273 (t0) cc_final: 0.6783 (t0) REVERT: d 230 MET cc_start: 0.7359 (mmm) cc_final: 0.7003 (mmm) REVERT: d 248 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8548 (p) REVERT: d 269 ASN cc_start: 0.8783 (t0) cc_final: 0.8561 (t0) outliers start: 150 outliers final: 106 residues processed: 1218 average time/residue: 0.2623 time to fit residues: 486.9308 Evaluate side-chains 1252 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 1130 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 216 TYR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 453 THR Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 617 ILE Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 267 GLU Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain H residue 275 MET Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 157 HIS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain J residue 598 GLU Chi-restraints excluded: chain J residue 611 GLN Chi-restraints excluded: chain c residue 33 MET Chi-restraints excluded: chain c residue 73 THR Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain c residue 174 GLU Chi-restraints excluded: chain c residue 241 SER Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 65 MET Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 135 SER Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 314 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain O residue 433 CYS Chi-restraints excluded: chain O residue 435 VAL Chi-restraints excluded: chain O residue 446 VAL Chi-restraints excluded: chain O residue 457 ILE Chi-restraints excluded: chain O residue 540 SER Chi-restraints excluded: chain O residue 547 GLN Chi-restraints excluded: chain O residue 647 ILE Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 227 SER Chi-restraints excluded: chain P residue 248 THR Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 271 ASP Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain Q residue 114 THR Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 157 HIS Chi-restraints excluded: chain Q residue 160 GLN Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 647 ILE Chi-restraints excluded: chain R residue 654 CYS Chi-restraints excluded: chain R residue 677 THR Chi-restraints excluded: chain R residue 679 MET Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Chi-restraints excluded: chain d residue 254 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 270 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 97 optimal weight: 0.1980 chunk 406 optimal weight: 0.2980 chunk 212 optimal weight: 3.9990 chunk 396 optimal weight: 0.0060 chunk 116 optimal weight: 0.9990 chunk 276 optimal weight: 1.9990 chunk 334 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 547 GLN ** G 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 190 GLN ** L 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 286 GLN O 323 GLN O 531 GLN ** P 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 143 HIS Q 157 HIS d 229 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.132397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111361 restraints weight = 72609.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.115250 restraints weight = 34832.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.117848 restraints weight = 21169.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.119481 restraints weight = 14802.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.120531 restraints weight = 11517.740| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34806 Z= 0.143 Angle : 0.687 16.610 47180 Z= 0.349 Chirality : 0.044 0.180 4964 Planarity : 0.005 0.099 6150 Dihedral : 4.931 43.947 4634 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.11 % Favored : 94.79 % Rotamer: Outliers : 4.14 % Allowed : 22.39 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.13), residues: 4110 helix: 0.39 (0.15), residues: 1140 sheet: -0.97 (0.18), residues: 790 loop : -0.40 (0.14), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 41 TYR 0.033 0.001 TYR N 67 PHE 0.027 0.001 PHE B 213 TRP 0.023 0.001 TRP E 191 HIS 0.008 0.001 HIS F 157 Details of bonding type rmsd covalent geometry : bond 0.00322 (34806) covalent geometry : angle 0.68690 (47180) hydrogen bonds : bond 0.03729 ( 1325) hydrogen bonds : angle 5.47924 ( 3786) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 1158 time to evaluate : 1.384 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: 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: A 7 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.6290 (mptp) REVERT: A 21 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8484 (p) REVERT: B 150 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7343 (t0) REVERT: B 215 VAL cc_start: 0.8728 (t) cc_final: 0.8499 (m) REVERT: B 218 LYS cc_start: 0.7874 (mttp) cc_final: 0.7633 (mttp) REVERT: B 226 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7038 (mt-10) REVERT: B 253 ASP cc_start: 0.7827 (t0) cc_final: 0.7499 (t0) REVERT: D 294 TRP cc_start: 0.7745 (t60) cc_final: 0.6354 (t60) REVERT: D 298 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7368 (mm-30) REVERT: D 301 LYS cc_start: 0.8765 (mtmt) cc_final: 0.8296 (mtmt) REVERT: D 323 ARG cc_start: 0.8403 (ttm110) cc_final: 0.8111 (ttm-80) REVERT: E 16 LEU cc_start: 0.8370 (tp) cc_final: 0.8157 (tt) REVERT: E 44 ARG cc_start: 0.7563 (ttp-110) cc_final: 0.7253 (ttp-110) REVERT: E 46 LYS cc_start: 0.7628 (tttm) cc_final: 0.7147 (tmtm) REVERT: E 74 MET cc_start: 0.6971 (mmp) cc_final: 0.6104 (mmm) REVERT: E 92 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7770 (t80) REVERT: E 97 MET cc_start: 0.5358 (mmt) cc_final: 0.4688 (mmt) REVERT: E 123 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6315 (mmp80) REVERT: E 175 GLU cc_start: 0.7212 (pp20) cc_final: 0.6963 (pp20) REVERT: E 195 ASN cc_start: 0.7701 (m110) cc_final: 0.7487 (t0) REVERT: F 44 TYR cc_start: 0.7931 (t80) cc_final: 0.7587 (t80) REVERT: F 59 TYR cc_start: 0.7205 (t80) cc_final: 0.6898 (t80) REVERT: F 67 TYR cc_start: 0.7500 (t80) cc_final: 0.6451 (t80) REVERT: F 98 GLN cc_start: 0.8330 (mm-40) cc_final: 0.7305 (mm-40) REVERT: F 116 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6727 (mt-10) REVERT: F 122 ARG cc_start: 0.8111 (mpp80) cc_final: 0.7593 (mtt90) REVERT: F 133 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.8720 (t) REVERT: F 142 VAL cc_start: 0.8721 (t) cc_final: 0.7866 (m) REVERT: F 147 GLU cc_start: 0.7435 (tt0) cc_final: 0.6845 (tt0) REVERT: F 156 ASN cc_start: 0.8300 (p0) cc_final: 0.7946 (p0) REVERT: G 251 ILE cc_start: 0.8172 (tt) cc_final: 0.7856 (tp) REVERT: G 257 ASP cc_start: 0.8013 (t70) cc_final: 0.7522 (t70) REVERT: G 276 MET cc_start: 0.6950 (mmm) cc_final: 0.6510 (mmm) REVERT: G 281 GLU cc_start: 0.8123 (pt0) cc_final: 0.7463 (pp20) REVERT: G 284 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7149 (mm-30) REVERT: G 316 GLU cc_start: 0.8256 (tt0) cc_final: 0.7769 (tt0) REVERT: G 332 GLU cc_start: 0.8211 (tp30) cc_final: 0.7941 (tp30) REVERT: G 335 ARG cc_start: 0.7347 (tpp80) cc_final: 0.6970 (tpp80) REVERT: G 345 ASP cc_start: 0.7648 (m-30) cc_final: 0.7275 (m-30) REVERT: G 351 ARG cc_start: 0.7395 (ttp-170) cc_final: 0.6998 (ttp-170) REVERT: G 373 ARG cc_start: 0.7810 (mpp80) cc_final: 0.7487 (mpp80) REVERT: G 428 TYR cc_start: 0.8329 (m-80) cc_final: 0.7269 (m-10) REVERT: G 451 ILE cc_start: 0.8284 (mt) cc_final: 0.7912 (mm) REVERT: G 537 GLU cc_start: 0.7532 (pp20) cc_final: 0.7325 (pp20) REVERT: G 592 LEU cc_start: 0.8213 (mm) cc_final: 0.7952 (tp) REVERT: G 656 GLU cc_start: 0.7770 (mp0) cc_final: 0.7554 (pm20) REVERT: G 688 GLN cc_start: 0.8668 (tp-100) cc_final: 0.7625 (tp40) REVERT: G 692 MET cc_start: 0.7554 (mmp) cc_final: 0.7243 (mmp) REVERT: H 39 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7821 (m-80) REVERT: H 56 ASP cc_start: 0.7955 (m-30) cc_final: 0.7701 (m-30) REVERT: H 110 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7326 (mm-30) REVERT: H 145 ASP cc_start: 0.7930 (t0) cc_final: 0.7582 (t0) REVERT: H 171 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7869 (ptm-80) REVERT: I 66 ARG cc_start: 0.7768 (ttm-80) cc_final: 0.7390 (ttm-80) REVERT: I 111 ASP cc_start: 0.7997 (m-30) cc_final: 0.7741 (m-30) REVERT: I 116 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7151 (mt-10) REVERT: I 122 ARG cc_start: 0.7862 (mpp80) cc_final: 0.6475 (mtt180) REVERT: I 125 GLN cc_start: 0.8411 (tp40) cc_final: 0.8074 (mm-40) REVERT: I 136 LYS cc_start: 0.8198 (mttt) cc_final: 0.7930 (mttt) REVERT: I 142 VAL cc_start: 0.8727 (t) cc_final: 0.8478 (p) REVERT: I 153 ILE cc_start: 0.8805 (mp) cc_final: 0.8166 (mt) REVERT: I 158 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7582 (ttm110) REVERT: I 185 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7257 (mt-10) REVERT: J 211 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7822 (mm-40) REVERT: J 216 TYR cc_start: 0.8481 (t80) cc_final: 0.8035 (t80) REVERT: J 218 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8149 (tt) REVERT: J 237 THR cc_start: 0.8723 (m) cc_final: 0.8510 (p) REVERT: J 256 GLN cc_start: 0.8370 (mt0) cc_final: 0.8061 (mm110) REVERT: J 260 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7244 (tmm) REVERT: J 322 GLU cc_start: 0.7944 (tp30) cc_final: 0.7346 (mp0) REVERT: J 619 GLN cc_start: 0.7286 (pm20) cc_final: 0.7072 (pm20) REVERT: J 640 LYS cc_start: 0.8527 (tptp) cc_final: 0.8324 (tptm) REVERT: c 24 ARG cc_start: 0.8195 (mmt-90) cc_final: 0.7750 (tpp80) REVERT: c 41 PHE cc_start: 0.9192 (m-80) cc_final: 0.8734 (m-80) REVERT: c 45 LEU cc_start: 0.8105 (mp) cc_final: 0.7861 (mt) REVERT: c 56 ASP cc_start: 0.8135 (m-30) cc_final: 0.7835 (m-30) REVERT: c 145 ASP cc_start: 0.8215 (m-30) cc_final: 0.7890 (m-30) REVERT: c 170 ASN cc_start: 0.7598 (t0) cc_final: 0.7324 (t0) REVERT: c 191 ARG cc_start: 0.7540 (mtp180) cc_final: 0.7239 (mtp180) REVERT: c 258 TYR cc_start: 0.8274 (p90) cc_final: 0.7854 (p90) REVERT: c 262 TYR cc_start: 0.8848 (t80) cc_final: 0.8262 (t80) REVERT: c 269 ASN cc_start: 0.8386 (t0) cc_final: 0.7952 (t0) REVERT: c 270 MET cc_start: 0.7602 (ppp) cc_final: 0.7153 (ppp) REVERT: c 271 ASP cc_start: 0.7777 (m-30) cc_final: 0.6819 (m-30) REVERT: C 7 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.6552 (tptt) REVERT: K 142 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7720 (ttp80) REVERT: K 153 PHE cc_start: 0.8231 (m-80) cc_final: 0.7852 (m-80) REVERT: K 253 ASP cc_start: 0.7786 (m-30) cc_final: 0.7557 (m-30) REVERT: K 287 LYS cc_start: 0.8392 (mtpt) cc_final: 0.8095 (mttp) REVERT: L 294 TRP cc_start: 0.7849 (t60) cc_final: 0.7080 (t60) REVERT: L 307 MET cc_start: 0.7501 (tpp) cc_final: 0.7094 (tpp) REVERT: L 310 ARG cc_start: 0.8022 (mtp180) cc_final: 0.7655 (mmm-85) REVERT: M 74 MET cc_start: 0.7744 (mmm) cc_final: 0.7394 (mmm) REVERT: M 88 LYS cc_start: 0.8016 (mmmm) cc_final: 0.7665 (tppp) REVERT: M 92 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7807 (t80) REVERT: M 96 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8407 (mm) REVERT: M 97 MET cc_start: 0.5884 (mmt) cc_final: 0.5489 (mmt) REVERT: M 158 LYS cc_start: 0.8360 (mttt) cc_final: 0.8043 (mttt) REVERT: M 191 TRP cc_start: 0.8162 (t-100) cc_final: 0.7956 (t-100) REVERT: M 193 MET cc_start: 0.7459 (mmm) cc_final: 0.6962 (tmm) REVERT: N 91 GLU cc_start: 0.7137 (mp0) cc_final: 0.6867 (mp0) REVERT: N 98 GLN cc_start: 0.8237 (mt0) cc_final: 0.7722 (mt0) REVERT: N 109 ASN cc_start: 0.8627 (p0) cc_final: 0.8252 (p0) REVERT: N 116 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7067 (mm-30) REVERT: N 136 LYS cc_start: 0.8575 (mttt) cc_final: 0.8304 (mtpp) REVERT: N 185 GLU cc_start: 0.7464 (tt0) cc_final: 0.6935 (tt0) REVERT: O 281 GLU cc_start: 0.8523 (pt0) cc_final: 0.8231 (pt0) REVERT: O 284 GLU cc_start: 0.7927 (tp30) cc_final: 0.7321 (tp30) REVERT: O 331 ASP cc_start: 0.8434 (p0) cc_final: 0.6552 (p0) REVERT: O 332 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7581 (tm-30) REVERT: O 350 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7536 (tm-30) REVERT: O 371 GLU cc_start: 0.7123 (tp30) cc_final: 0.6465 (tp30) REVERT: O 438 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7923 (mtp85) REVERT: O 502 TYR cc_start: 0.6240 (p90) cc_final: 0.4793 (p90) REVERT: O 547 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8174 (mt0) REVERT: O 688 GLN cc_start: 0.8553 (tm-30) cc_final: 0.7997 (tm-30) REVERT: O 692 MET cc_start: 0.7745 (mtm) cc_final: 0.7101 (mtm) REVERT: P 28 LEU cc_start: 0.8633 (tp) cc_final: 0.8135 (mm) REVERT: P 43 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7203 (mtm-85) REVERT: P 94 MET cc_start: 0.7439 (mmp) cc_final: 0.7129 (mmp) REVERT: P 180 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7730 (mt-10) REVERT: P 267 GLU cc_start: 0.6992 (mp0) cc_final: 0.6064 (mp0) REVERT: Q 59 TYR cc_start: 0.7314 (t80) cc_final: 0.6973 (t80) REVERT: Q 116 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7012 (mt-10) REVERT: Q 121 GLN cc_start: 0.6317 (mp10) cc_final: 0.5738 (mp10) REVERT: Q 122 ARG cc_start: 0.8035 (mpp80) cc_final: 0.7822 (mpp80) REVERT: Q 151 GLU cc_start: 0.7595 (tp30) cc_final: 0.6901 (tp30) REVERT: Q 160 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.7045 (mm-40) REVERT: Q 173 LYS cc_start: 0.8444 (ptpp) cc_final: 0.7687 (ptpp) REVERT: Q 181 GLU cc_start: 0.7626 (tt0) cc_final: 0.7169 (tt0) REVERT: R 205 MET cc_start: 0.5292 (tpt) cc_final: 0.4429 (tpt) REVERT: R 207 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.6364 (mp0) REVERT: R 242 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7445 (tm-30) REVERT: R 260 MET cc_start: 0.7799 (tpp) cc_final: 0.7478 (tpp) REVERT: R 313 ASN cc_start: 0.8239 (t0) cc_final: 0.7971 (t0) REVERT: R 316 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8042 (tm-30) REVERT: R 322 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7373 (tm-30) REVERT: R 334 TYR cc_start: 0.8243 (t80) cc_final: 0.7892 (t80) REVERT: R 335 ARG cc_start: 0.8411 (mmt90) cc_final: 0.8156 (mtt-85) REVERT: R 371 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7234 (tm-30) REVERT: R 373 ARG cc_start: 0.6836 (ptp90) cc_final: 0.6376 (ptp90) REVERT: R 433 CYS cc_start: 0.7756 (p) cc_final: 0.7407 (p) REVERT: R 438 ARG cc_start: 0.8751 (tpp80) cc_final: 0.8194 (mtt90) REVERT: R 455 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8290 (ttm-80) REVERT: R 470 ILE cc_start: 0.8854 (mm) cc_final: 0.8446 (pt) REVERT: R 530 ILE cc_start: 0.8886 (mm) cc_final: 0.8478 (tp) REVERT: R 556 ASN cc_start: 0.8802 (m-40) cc_final: 0.8578 (m-40) REVERT: R 605 ILE cc_start: 0.8755 (mt) cc_final: 0.8316 (pt) REVERT: R 616 LEU cc_start: 0.8715 (mm) cc_final: 0.8500 (mt) REVERT: R 640 LYS cc_start: 0.8656 (tptt) cc_final: 0.8364 (tptm) REVERT: R 679 MET cc_start: 0.4356 (OUTLIER) cc_final: 0.3928 (tmm) REVERT: d 28 LEU cc_start: 0.8611 (tp) cc_final: 0.8400 (tt) REVERT: d 33 MET cc_start: 0.7912 (tpp) cc_final: 0.7622 (tpp) REVERT: d 38 ASP cc_start: 0.8091 (m-30) cc_final: 0.7705 (m-30) REVERT: d 43 ARG cc_start: 0.8174 (ttp80) cc_final: 0.7604 (ttp80) REVERT: d 56 ASP cc_start: 0.8322 (m-30) cc_final: 0.8082 (m-30) REVERT: d 81 GLU cc_start: 0.7553 (mt-10) cc_final: 0.6975 (mt-10) REVERT: d 102 ARG cc_start: 0.7830 (mtp85) cc_final: 0.6895 (mtp85) REVERT: d 170 ASN cc_start: 0.7745 (t0) cc_final: 0.7122 (t0) REVERT: d 180 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7218 (mm-30) REVERT: d 183 LYS cc_start: 0.8764 (mtmt) cc_final: 0.8388 (ptpp) REVERT: d 220 ASP cc_start: 0.7315 (t0) cc_final: 0.6838 (t0) REVERT: d 248 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8504 (p) REVERT: d 262 TYR cc_start: 0.8885 (t80) cc_final: 0.8398 (t80) REVERT: d 269 ASN cc_start: 0.8591 (t0) cc_final: 0.8357 (t0) outliers start: 151 outliers final: 109 residues processed: 1209 average time/residue: 0.2716 time to fit residues: 497.7689 Evaluate side-chains 1257 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1128 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 16 GLN Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 453 THR Chi-restraints excluded: chain G residue 456 LYS Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 267 GLU Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 157 HIS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 230 ASP Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain J residue 598 GLU Chi-restraints excluded: chain J residue 611 GLN Chi-restraints excluded: chain c residue 33 MET Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain c residue 172 THR Chi-restraints excluded: chain c residue 174 GLU Chi-restraints excluded: chain c residue 241 SER Chi-restraints excluded: chain c residue 248 THR Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 65 MET Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 314 VAL Chi-restraints excluded: chain O residue 433 CYS Chi-restraints excluded: chain O residue 457 ILE Chi-restraints excluded: chain O residue 547 GLN Chi-restraints excluded: chain O residue 647 ILE Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 172 THR Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 248 THR Chi-restraints excluded: chain P residue 250 TYR Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 271 ASP Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain Q residue 114 THR Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 157 HIS Chi-restraints excluded: chain Q residue 160 GLN Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 455 ARG Chi-restraints excluded: chain R residue 456 LYS Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 654 CYS Chi-restraints excluded: chain R residue 677 THR Chi-restraints excluded: chain R residue 679 MET Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 228 ILE Chi-restraints excluded: chain d residue 229 GLN Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Chi-restraints excluded: chain d residue 254 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 367 optimal weight: 0.0050 chunk 365 optimal weight: 2.9990 chunk 391 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 341 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 chunk 223 optimal weight: 0.6980 chunk 258 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN G 547 GLN ** G 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 HIS J 323 GLN J 342 GLN J 541 ASN ** c 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 146 GLN c 234 ASN c 257 ASN K 190 GLN ** N 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 286 GLN O 323 GLN O 531 GLN O 552 GLN ** P 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 ASN Q 157 HIS ** R 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.132605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111724 restraints weight = 72473.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.115609 restraints weight = 34716.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.118172 restraints weight = 21043.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.119499 restraints weight = 14737.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.120846 restraints weight = 11883.634| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 34806 Z= 0.166 Angle : 0.703 13.517 47180 Z= 0.358 Chirality : 0.044 0.191 4964 Planarity : 0.005 0.097 6150 Dihedral : 4.949 44.089 4634 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.26 % Favored : 94.65 % Rotamer: Outliers : 3.81 % Allowed : 22.94 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.13), residues: 4110 helix: 0.34 (0.15), residues: 1143 sheet: -1.01 (0.17), residues: 821 loop : -0.39 (0.14), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 41 TYR 0.022 0.001 TYR M 160 PHE 0.028 0.001 PHE B 213 TRP 0.018 0.001 TRP E 191 HIS 0.007 0.001 HIS F 157 Details of bonding type rmsd covalent geometry : bond 0.00375 (34806) covalent geometry : angle 0.70252 (47180) hydrogen bonds : bond 0.03826 ( 1325) hydrogen bonds : angle 5.47970 ( 3786) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 1173 time to evaluate : 1.501 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.6288 (mptp) REVERT: A 20 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7235 (tm-30) REVERT: A 21 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8491 (p) REVERT: B 144 LEU cc_start: 0.7947 (tp) cc_final: 0.7740 (mt) REVERT: B 150 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7366 (t0) REVERT: B 215 VAL cc_start: 0.8685 (t) cc_final: 0.8445 (m) REVERT: B 218 LYS cc_start: 0.7868 (mttp) cc_final: 0.7593 (mttp) REVERT: B 226 GLU cc_start: 0.7344 (mt-10) cc_final: 0.7016 (mt-10) REVERT: B 253 ASP cc_start: 0.7834 (t0) cc_final: 0.7452 (t0) REVERT: D 294 TRP cc_start: 0.7780 (t60) cc_final: 0.6739 (t60) REVERT: D 298 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7839 (mm-30) REVERT: D 301 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8250 (mtmt) REVERT: D 307 MET cc_start: 0.7193 (tpp) cc_final: 0.6940 (tpp) REVERT: D 323 ARG cc_start: 0.8439 (ttm110) cc_final: 0.8144 (ttm-80) REVERT: E 44 ARG cc_start: 0.7590 (ttp-110) cc_final: 0.7248 (ttp-110) REVERT: E 46 LYS cc_start: 0.7668 (tttm) cc_final: 0.7193 (tmtm) REVERT: E 74 MET cc_start: 0.6999 (mmp) cc_final: 0.6149 (mmm) REVERT: E 92 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7793 (t80) REVERT: E 97 MET cc_start: 0.5445 (mmt) cc_final: 0.4715 (mmt) REVERT: E 123 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.6290 (mmp80) REVERT: E 195 ASN cc_start: 0.7789 (m110) cc_final: 0.7548 (t0) REVERT: F 44 TYR cc_start: 0.7942 (t80) cc_final: 0.7596 (t80) REVERT: F 59 TYR cc_start: 0.7211 (t80) cc_final: 0.6901 (t80) REVERT: F 67 TYR cc_start: 0.7531 (t80) cc_final: 0.6551 (t80) REVERT: F 98 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7240 (mm-40) REVERT: F 116 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6805 (mt-10) REVERT: F 122 ARG cc_start: 0.8152 (mpp80) cc_final: 0.7652 (mtt90) REVERT: F 142 VAL cc_start: 0.8725 (t) cc_final: 0.7822 (m) REVERT: F 147 GLU cc_start: 0.7393 (tt0) cc_final: 0.6832 (tt0) REVERT: F 156 ASN cc_start: 0.8325 (p0) cc_final: 0.8059 (p0) REVERT: F 164 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6597 (mtm) REVERT: G 251 ILE cc_start: 0.8201 (tt) cc_final: 0.7886 (tp) REVERT: G 257 ASP cc_start: 0.8027 (t70) cc_final: 0.7526 (t70) REVERT: G 276 MET cc_start: 0.6988 (mmm) cc_final: 0.6562 (mmm) REVERT: G 281 GLU cc_start: 0.8117 (pt0) cc_final: 0.7466 (pp20) REVERT: G 284 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7246 (mm-30) REVERT: G 316 GLU cc_start: 0.8238 (tt0) cc_final: 0.7756 (tt0) REVERT: G 332 GLU cc_start: 0.8231 (tp30) cc_final: 0.7769 (tm-30) REVERT: G 335 ARG cc_start: 0.7326 (tpp80) cc_final: 0.6994 (tpp80) REVERT: G 345 ASP cc_start: 0.7668 (m-30) cc_final: 0.7302 (m-30) REVERT: G 351 ARG cc_start: 0.7411 (ttp-170) cc_final: 0.7071 (ttp-170) REVERT: G 428 TYR cc_start: 0.8271 (m-80) cc_final: 0.7181 (m-10) REVERT: G 451 ILE cc_start: 0.8293 (mt) cc_final: 0.7913 (mm) REVERT: G 537 GLU cc_start: 0.7505 (pp20) cc_final: 0.7297 (pp20) REVERT: G 592 LEU cc_start: 0.8216 (mm) cc_final: 0.7981 (tp) REVERT: G 656 GLU cc_start: 0.7780 (mp0) cc_final: 0.7565 (pm20) REVERT: G 688 GLN cc_start: 0.8669 (tp-100) cc_final: 0.7615 (tp40) REVERT: G 692 MET cc_start: 0.7531 (mmp) cc_final: 0.7217 (mmp) REVERT: H 39 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: H 110 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7319 (mm-30) REVERT: H 145 ASP cc_start: 0.7922 (t0) cc_final: 0.7595 (t0) REVERT: H 171 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7924 (ptm-80) REVERT: I 66 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7398 (ttm-80) REVERT: I 111 ASP cc_start: 0.8021 (m-30) cc_final: 0.7778 (m-30) REVERT: I 116 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7227 (mt-10) REVERT: I 122 ARG cc_start: 0.7861 (mpp80) cc_final: 0.6525 (mtt90) REVERT: I 125 GLN cc_start: 0.8426 (tp40) cc_final: 0.8100 (mm-40) REVERT: I 136 LYS cc_start: 0.8206 (mttt) cc_final: 0.7951 (mttt) REVERT: I 142 VAL cc_start: 0.8730 (t) cc_final: 0.8484 (p) REVERT: I 153 ILE cc_start: 0.8792 (mp) cc_final: 0.8097 (mt) REVERT: I 158 ARG cc_start: 0.8226 (ttm110) cc_final: 0.7565 (ttm110) REVERT: I 185 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7288 (mt-10) REVERT: J 211 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7823 (mm-40) REVERT: J 216 TYR cc_start: 0.8509 (t80) cc_final: 0.8051 (t80) REVERT: J 237 THR cc_start: 0.8742 (m) cc_final: 0.8532 (p) REVERT: J 256 GLN cc_start: 0.8392 (mt0) cc_final: 0.8094 (mm110) REVERT: J 260 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7211 (tmm) REVERT: J 322 GLU cc_start: 0.7932 (tp30) cc_final: 0.7392 (mp0) REVERT: J 640 LYS cc_start: 0.8527 (tptp) cc_final: 0.8325 (tptm) REVERT: c 24 ARG cc_start: 0.8202 (mmt-90) cc_final: 0.7739 (tpp80) REVERT: c 41 PHE cc_start: 0.9197 (m-80) cc_final: 0.8766 (m-80) REVERT: c 45 LEU cc_start: 0.8148 (mp) cc_final: 0.7927 (mt) REVERT: c 145 ASP cc_start: 0.8204 (m-30) cc_final: 0.7800 (m-30) REVERT: c 170 ASN cc_start: 0.7585 (t0) cc_final: 0.7303 (t0) REVERT: c 191 ARG cc_start: 0.7563 (mtp180) cc_final: 0.7271 (mtp180) REVERT: c 258 TYR cc_start: 0.8284 (p90) cc_final: 0.7867 (p90) REVERT: c 262 TYR cc_start: 0.8859 (t80) cc_final: 0.8137 (t80) REVERT: c 269 ASN cc_start: 0.8365 (t0) cc_final: 0.7828 (t0) REVERT: c 270 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7127 (ppp) REVERT: c 271 ASP cc_start: 0.7732 (m-30) cc_final: 0.6772 (m-30) REVERT: C 7 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.6692 (tptt) REVERT: K 153 PHE cc_start: 0.8231 (m-80) cc_final: 0.7842 (m-80) REVERT: K 183 ASP cc_start: 0.6402 (t0) cc_final: 0.5945 (t0) REVERT: K 253 ASP cc_start: 0.7912 (m-30) cc_final: 0.7647 (m-30) REVERT: K 287 LYS cc_start: 0.8418 (mtpt) cc_final: 0.8106 (mttp) REVERT: L 294 TRP cc_start: 0.7909 (t60) cc_final: 0.7132 (t60) REVERT: L 307 MET cc_start: 0.7518 (tpp) cc_final: 0.7100 (tpp) REVERT: L 323 ARG cc_start: 0.8307 (ttm110) cc_final: 0.7950 (ttm-80) REVERT: M 35 LEU cc_start: 0.8862 (mt) cc_final: 0.8648 (mm) REVERT: M 47 LEU cc_start: 0.7428 (mm) cc_final: 0.6918 (mp) REVERT: M 88 LYS cc_start: 0.8061 (mmmm) cc_final: 0.7707 (tppp) REVERT: M 92 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.7735 (t80) REVERT: M 95 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7625 (mt-10) REVERT: M 96 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8360 (mm) REVERT: M 97 MET cc_start: 0.5941 (mmt) cc_final: 0.5516 (mmt) REVERT: M 158 LYS cc_start: 0.8397 (mttt) cc_final: 0.8051 (mttt) REVERT: M 193 MET cc_start: 0.7517 (mmm) cc_final: 0.7033 (tmm) REVERT: N 91 GLU cc_start: 0.7102 (mp0) cc_final: 0.6768 (mp0) REVERT: N 98 GLN cc_start: 0.8252 (mt0) cc_final: 0.7755 (mt0) REVERT: N 109 ASN cc_start: 0.8624 (p0) cc_final: 0.8234 (p0) REVERT: N 116 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7089 (mm-30) REVERT: N 136 LYS cc_start: 0.8569 (mttt) cc_final: 0.8299 (mtpp) REVERT: N 185 GLU cc_start: 0.7413 (tt0) cc_final: 0.6843 (tt0) REVERT: N 195 GLU cc_start: 0.5304 (mm-30) cc_final: 0.4918 (mm-30) REVERT: N 196 GLU cc_start: 0.8156 (mp0) cc_final: 0.7903 (mp0) REVERT: O 281 GLU cc_start: 0.8518 (pt0) cc_final: 0.8191 (pt0) REVERT: O 284 GLU cc_start: 0.7930 (tp30) cc_final: 0.7320 (tp30) REVERT: O 316 GLU cc_start: 0.8307 (tt0) cc_final: 0.8092 (tt0) REVERT: O 347 HIS cc_start: 0.8800 (m170) cc_final: 0.8582 (m170) REVERT: O 350 GLN cc_start: 0.8360 (tm-30) cc_final: 0.7586 (tm-30) REVERT: O 371 GLU cc_start: 0.7161 (tp30) cc_final: 0.6560 (tp30) REVERT: O 373 ARG cc_start: 0.7765 (mpp80) cc_final: 0.7195 (mpp80) REVERT: O 502 TYR cc_start: 0.6251 (p90) cc_final: 0.4863 (p90) REVERT: O 547 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8150 (mt0) REVERT: O 688 GLN cc_start: 0.8509 (tm-30) cc_final: 0.7902 (tm-30) REVERT: O 692 MET cc_start: 0.7785 (mtm) cc_final: 0.7153 (mtm) REVERT: P 28 LEU cc_start: 0.8628 (tp) cc_final: 0.8118 (mm) REVERT: P 43 ARG cc_start: 0.7943 (mtm-85) cc_final: 0.7171 (mtm-85) REVERT: P 94 MET cc_start: 0.7425 (mmp) cc_final: 0.7130 (mmp) REVERT: P 102 ARG cc_start: 0.8309 (mtp85) cc_final: 0.8066 (mmm160) REVERT: P 180 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7732 (mt-10) REVERT: P 267 GLU cc_start: 0.6942 (mp0) cc_final: 0.6088 (mp0) REVERT: Q 19 GLU cc_start: 0.5594 (pt0) cc_final: 0.3914 (pt0) REVERT: Q 37 ARG cc_start: 0.6978 (ttp80) cc_final: 0.6544 (ttp80) REVERT: Q 59 TYR cc_start: 0.7342 (t80) cc_final: 0.6995 (t80) REVERT: Q 116 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7020 (mt-10) REVERT: Q 121 GLN cc_start: 0.6355 (mp10) cc_final: 0.5723 (mp10) REVERT: Q 151 GLU cc_start: 0.7617 (tp30) cc_final: 0.6131 (tp30) REVERT: Q 158 ARG cc_start: 0.7219 (mtt-85) cc_final: 0.7001 (ttm110) REVERT: Q 160 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7077 (mm-40) REVERT: Q 173 LYS cc_start: 0.8488 (ptpp) cc_final: 0.7697 (ptpp) REVERT: Q 181 GLU cc_start: 0.7698 (tt0) cc_final: 0.7199 (tt0) REVERT: R 205 MET cc_start: 0.5298 (tpt) cc_final: 0.4512 (tpt) REVERT: R 207 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.6481 (mp0) REVERT: R 259 LYS cc_start: 0.8985 (mmtp) cc_final: 0.8614 (mttp) REVERT: R 260 MET cc_start: 0.7816 (tpp) cc_final: 0.7502 (tpp) REVERT: R 313 ASN cc_start: 0.8241 (t0) cc_final: 0.7918 (t0) REVERT: R 322 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7493 (tm-30) REVERT: R 334 TYR cc_start: 0.8296 (t80) cc_final: 0.7913 (t80) REVERT: R 371 GLU cc_start: 0.7499 (tm-30) cc_final: 0.6897 (tm-30) REVERT: R 433 CYS cc_start: 0.7817 (p) cc_final: 0.7444 (p) REVERT: R 438 ARG cc_start: 0.8765 (tpp80) cc_final: 0.8233 (mtt90) REVERT: R 455 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7733 (ttm170) REVERT: R 470 ILE cc_start: 0.8853 (mm) cc_final: 0.8517 (pt) REVERT: R 503 GLN cc_start: 0.7564 (pm20) cc_final: 0.6727 (pm20) REVERT: R 522 GLU cc_start: 0.7439 (pm20) cc_final: 0.7146 (pm20) REVERT: R 530 ILE cc_start: 0.8889 (mm) cc_final: 0.8456 (tp) REVERT: R 556 ASN cc_start: 0.8804 (m-40) cc_final: 0.8583 (m-40) REVERT: R 605 ILE cc_start: 0.8762 (mt) cc_final: 0.8328 (pt) REVERT: R 616 LEU cc_start: 0.8716 (mm) cc_final: 0.8492 (mt) REVERT: R 640 LYS cc_start: 0.8659 (tptt) cc_final: 0.8368 (tptm) REVERT: R 679 MET cc_start: 0.4434 (tmm) cc_final: 0.3872 (tmm) REVERT: d 33 MET cc_start: 0.7936 (tpp) cc_final: 0.7630 (tpp) REVERT: d 38 ASP cc_start: 0.8023 (m-30) cc_final: 0.7709 (m-30) REVERT: d 43 ARG cc_start: 0.8166 (ttp80) cc_final: 0.7612 (ttp80) REVERT: d 81 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6990 (mt-10) REVERT: d 102 ARG cc_start: 0.7815 (mtp85) cc_final: 0.6913 (mtp85) REVERT: d 170 ASN cc_start: 0.7756 (t0) cc_final: 0.7139 (t0) REVERT: d 180 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7204 (mm-30) REVERT: d 183 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8367 (ptpp) REVERT: d 220 ASP cc_start: 0.7348 (t0) cc_final: 0.7032 (t0) REVERT: d 248 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8537 (p) REVERT: d 269 ASN cc_start: 0.8369 (t0) cc_final: 0.8090 (t0) outliers start: 139 outliers final: 112 residues processed: 1218 average time/residue: 0.2657 time to fit residues: 492.7296 Evaluate side-chains 1278 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1148 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 453 THR Chi-restraints excluded: chain G residue 456 LYS Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 267 GLU Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 42 ASP Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 157 HIS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain J residue 587 GLU Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain J residue 598 GLU Chi-restraints excluded: chain J residue 611 GLN Chi-restraints excluded: chain c residue 33 MET Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain c residue 172 THR Chi-restraints excluded: chain c residue 174 GLU Chi-restraints excluded: chain c residue 241 SER Chi-restraints excluded: chain c residue 248 THR Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 270 MET Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 65 MET Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 314 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain O residue 433 CYS Chi-restraints excluded: chain O residue 446 VAL Chi-restraints excluded: chain O residue 457 ILE Chi-restraints excluded: chain O residue 547 GLN Chi-restraints excluded: chain O residue 647 ILE Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 172 THR Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 227 SER Chi-restraints excluded: chain P residue 248 THR Chi-restraints excluded: chain P residue 250 TYR Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 271 ASP Chi-restraints excluded: chain Q residue 20 TYR Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain Q residue 114 THR Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 157 HIS Chi-restraints excluded: chain Q residue 160 GLN Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 455 ARG Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 654 CYS Chi-restraints excluded: chain R residue 677 THR Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 399 optimal weight: 3.9990 chunk 391 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 394 optimal weight: 5.9990 chunk 256 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 287 optimal weight: 0.7980 chunk 226 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 278 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN G 231 HIS G 547 GLN ** G 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 HIS ** I 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 234 ASN c 257 ASN ** N 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 231 HIS O 286 GLN O 426 ASN ** O 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 157 HIS ** R 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.128833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107726 restraints weight = 72589.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.111579 restraints weight = 34865.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.114068 restraints weight = 21232.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115831 restraints weight = 15027.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116743 restraints weight = 11562.511| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 34806 Z= 0.246 Angle : 0.770 13.418 47180 Z= 0.391 Chirality : 0.046 0.215 4964 Planarity : 0.005 0.091 6150 Dihedral : 5.129 45.153 4634 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.94 % Favored : 93.94 % Rotamer: Outliers : 4.23 % Allowed : 23.57 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.13), residues: 4110 helix: 0.24 (0.15), residues: 1145 sheet: -1.11 (0.17), residues: 813 loop : -0.43 (0.14), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG d 232 TYR 0.026 0.002 TYR J 667 PHE 0.038 0.002 PHE R 321 TRP 0.036 0.002 TRP M 191 HIS 0.031 0.001 HIS Q 157 Details of bonding type rmsd covalent geometry : bond 0.00542 (34806) covalent geometry : angle 0.77034 (47180) hydrogen bonds : bond 0.04125 ( 1325) hydrogen bonds : angle 5.60572 ( 3786) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1192 time to evaluate : 1.105 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: 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: A 6 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8682 (tp) REVERT: A 7 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.6373 (tptp) REVERT: A 20 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7332 (tm-30) REVERT: A 21 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8514 (p) REVERT: B 144 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7778 (mt) REVERT: B 150 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7321 (t0) REVERT: B 180 LEU cc_start: 0.7389 (mt) cc_final: 0.7128 (mt) REVERT: B 215 VAL cc_start: 0.8707 (t) cc_final: 0.8427 (m) REVERT: B 218 LYS cc_start: 0.7893 (mttp) cc_final: 0.7611 (mttp) REVERT: B 226 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6996 (mt-10) REVERT: B 253 ASP cc_start: 0.7822 (t0) cc_final: 0.7419 (t0) REVERT: D 294 TRP cc_start: 0.7874 (t60) cc_final: 0.6833 (t60) REVERT: D 298 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7700 (mm-30) REVERT: D 307 MET cc_start: 0.7237 (tpp) cc_final: 0.6997 (tpp) REVERT: D 323 ARG cc_start: 0.8466 (ttm110) cc_final: 0.8162 (ttm-80) REVERT: E 16 LEU cc_start: 0.8280 (tp) cc_final: 0.8074 (tt) REVERT: E 26 LYS cc_start: 0.8122 (mttm) cc_final: 0.7904 (mttm) REVERT: E 44 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.7285 (ttp-110) REVERT: E 46 LYS cc_start: 0.7713 (tttm) cc_final: 0.7235 (tmtm) REVERT: E 74 MET cc_start: 0.7087 (mmp) cc_final: 0.6162 (mmm) REVERT: E 92 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7796 (t80) REVERT: E 97 MET cc_start: 0.5595 (mmt) cc_final: 0.4831 (mmt) REVERT: E 123 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6318 (mmp80) REVERT: E 175 GLU cc_start: 0.7374 (pp20) cc_final: 0.7040 (pp20) REVERT: F 44 TYR cc_start: 0.7843 (t80) cc_final: 0.7543 (t80) REVERT: F 59 TYR cc_start: 0.7241 (t80) cc_final: 0.6969 (t80) REVERT: F 67 TYR cc_start: 0.7648 (t80) cc_final: 0.6738 (t80) REVERT: F 98 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7159 (mm-40) REVERT: F 122 ARG cc_start: 0.8248 (mpp80) cc_final: 0.7659 (mtt90) REVERT: F 142 VAL cc_start: 0.8758 (t) cc_final: 0.7893 (m) REVERT: F 147 GLU cc_start: 0.7529 (tt0) cc_final: 0.6822 (tt0) REVERT: F 156 ASN cc_start: 0.8413 (p0) cc_final: 0.8192 (p0) REVERT: G 251 ILE cc_start: 0.8298 (tt) cc_final: 0.7989 (tp) REVERT: G 257 ASP cc_start: 0.8045 (t70) cc_final: 0.7538 (t70) REVERT: G 276 MET cc_start: 0.7062 (mmm) cc_final: 0.6623 (mmm) REVERT: G 281 GLU cc_start: 0.8154 (pt0) cc_final: 0.7561 (pp20) REVERT: G 284 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7357 (mm-30) REVERT: G 287 LYS cc_start: 0.8843 (mmmt) cc_final: 0.8593 (mmmt) REVERT: G 316 GLU cc_start: 0.8230 (tt0) cc_final: 0.7775 (tt0) REVERT: G 332 GLU cc_start: 0.8241 (tp30) cc_final: 0.7834 (tm-30) REVERT: G 351 ARG cc_start: 0.7394 (ttp-170) cc_final: 0.7077 (ttp-170) REVERT: G 428 TYR cc_start: 0.8356 (m-80) cc_final: 0.7244 (m-10) REVERT: G 451 ILE cc_start: 0.8313 (mt) cc_final: 0.7938 (mm) REVERT: G 592 LEU cc_start: 0.8237 (mm) cc_final: 0.8003 (tp) REVERT: G 666 VAL cc_start: 0.8236 (p) cc_final: 0.7891 (p) REVERT: G 667 TYR cc_start: 0.6642 (m-10) cc_final: 0.6294 (m-10) REVERT: G 688 GLN cc_start: 0.8630 (tp-100) cc_final: 0.7589 (tp40) REVERT: G 692 MET cc_start: 0.7573 (mmp) cc_final: 0.7235 (mmp) REVERT: H 39 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7984 (m-80) REVERT: H 110 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7348 (mm-30) REVERT: H 145 ASP cc_start: 0.7967 (t0) cc_final: 0.7617 (t0) REVERT: H 149 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8467 (mtpp) REVERT: H 171 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8042 (ptm-80) REVERT: I 66 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7378 (ttm-80) REVERT: I 111 ASP cc_start: 0.8037 (m-30) cc_final: 0.7782 (m-30) REVERT: I 116 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7247 (mt-10) REVERT: I 121 GLN cc_start: 0.6181 (mp-120) cc_final: 0.5943 (mp-120) REVERT: I 122 ARG cc_start: 0.7894 (mpp80) cc_final: 0.6669 (mtt90) REVERT: I 136 LYS cc_start: 0.8246 (mttt) cc_final: 0.7989 (mttt) REVERT: I 142 VAL cc_start: 0.8765 (t) cc_final: 0.8526 (p) REVERT: I 153 ILE cc_start: 0.8815 (mp) cc_final: 0.8096 (mt) REVERT: I 158 ARG cc_start: 0.8238 (ttm110) cc_final: 0.7524 (ttm110) REVERT: I 185 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7231 (mt-10) REVERT: J 211 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7820 (mm-40) REVERT: J 216 TYR cc_start: 0.8638 (t80) cc_final: 0.8160 (t80) REVERT: J 237 THR cc_start: 0.8776 (m) cc_final: 0.8559 (p) REVERT: J 256 GLN cc_start: 0.8426 (mt0) cc_final: 0.8131 (mm110) REVERT: J 260 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7171 (tmm) REVERT: J 313 ASN cc_start: 0.8202 (t0) cc_final: 0.7762 (t0) REVERT: J 322 GLU cc_start: 0.8007 (tp30) cc_final: 0.7470 (mp0) REVERT: J 438 ARG cc_start: 0.8845 (tpp80) cc_final: 0.8600 (mpp80) REVERT: J 619 GLN cc_start: 0.7158 (pm20) cc_final: 0.6858 (pm20) REVERT: J 620 TYR cc_start: 0.8148 (m-80) cc_final: 0.7768 (m-80) REVERT: J 640 LYS cc_start: 0.8566 (tptp) cc_final: 0.8365 (tptm) REVERT: c 24 ARG cc_start: 0.8220 (mmt-90) cc_final: 0.7784 (tpp80) REVERT: c 45 LEU cc_start: 0.8230 (mp) cc_final: 0.8011 (mt) REVERT: c 56 ASP cc_start: 0.8120 (m-30) cc_final: 0.7917 (m-30) REVERT: c 145 ASP cc_start: 0.8139 (m-30) cc_final: 0.7740 (m-30) REVERT: c 170 ASN cc_start: 0.7584 (t0) cc_final: 0.7349 (t0) REVERT: c 183 LYS cc_start: 0.8401 (mtpp) cc_final: 0.8071 (mtmm) REVERT: c 191 ARG cc_start: 0.7590 (mtp180) cc_final: 0.7316 (mtp180) REVERT: c 258 TYR cc_start: 0.8348 (p90) cc_final: 0.7995 (p90) REVERT: c 262 TYR cc_start: 0.8912 (t80) cc_final: 0.8171 (t80) REVERT: c 269 ASN cc_start: 0.8408 (t0) cc_final: 0.7872 (t0) REVERT: c 270 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7088 (ppp) REVERT: c 271 ASP cc_start: 0.7681 (m-30) cc_final: 0.6762 (m-30) REVERT: C 7 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.6709 (tptt) REVERT: K 189 ARG cc_start: 0.7874 (mtp85) cc_final: 0.7638 (mmt90) REVERT: K 210 ASP cc_start: 0.7971 (t0) cc_final: 0.7721 (t0) REVERT: K 287 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8121 (mttp) REVERT: K 295 ASP cc_start: 0.6894 (t0) cc_final: 0.6660 (t0) REVERT: L 294 TRP cc_start: 0.8015 (t60) cc_final: 0.6977 (t60) REVERT: L 298 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7779 (mm-30) REVERT: L 307 MET cc_start: 0.7560 (tpp) cc_final: 0.7163 (tpp) REVERT: M 27 GLU cc_start: 0.7775 (tt0) cc_final: 0.7363 (tm-30) REVERT: M 47 LEU cc_start: 0.7466 (mm) cc_final: 0.6850 (mp) REVERT: M 86 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6019 (ptp-170) REVERT: M 88 LYS cc_start: 0.8199 (mmmm) cc_final: 0.7794 (tppp) REVERT: M 92 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7725 (t80) REVERT: M 95 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7608 (mt-10) REVERT: M 96 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8366 (mm) REVERT: M 97 MET cc_start: 0.5966 (mmt) cc_final: 0.5515 (mmt) REVERT: M 142 MET cc_start: 0.7876 (tpp) cc_final: 0.7663 (tpp) REVERT: M 158 LYS cc_start: 0.8488 (mttt) cc_final: 0.8121 (mttt) REVERT: M 193 MET cc_start: 0.7538 (mmm) cc_final: 0.7063 (tmm) REVERT: N 91 GLU cc_start: 0.7123 (mp0) cc_final: 0.6802 (mp0) REVERT: N 98 GLN cc_start: 0.8255 (mt0) cc_final: 0.7725 (mt0) REVERT: N 116 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7152 (mm-30) REVERT: N 136 LYS cc_start: 0.8566 (mttt) cc_final: 0.8302 (mtpp) REVERT: N 185 GLU cc_start: 0.7416 (tt0) cc_final: 0.6841 (tt0) REVERT: N 196 GLU cc_start: 0.8190 (mp0) cc_final: 0.7925 (mp0) REVERT: O 207 GLU cc_start: 0.7834 (pm20) cc_final: 0.7632 (pm20) REVERT: O 281 GLU cc_start: 0.8532 (pt0) cc_final: 0.8217 (pt0) REVERT: O 284 GLU cc_start: 0.8004 (tp30) cc_final: 0.7404 (tp30) REVERT: O 316 GLU cc_start: 0.8356 (tt0) cc_final: 0.8114 (tt0) REVERT: O 350 GLN cc_start: 0.8379 (tm-30) cc_final: 0.7660 (tm-30) REVERT: O 371 GLU cc_start: 0.7186 (tp30) cc_final: 0.6611 (tp30) REVERT: O 373 ARG cc_start: 0.7781 (mpp80) cc_final: 0.7346 (mpp80) REVERT: O 502 TYR cc_start: 0.6238 (p90) cc_final: 0.4716 (p90) REVERT: O 643 GLU cc_start: 0.7479 (pm20) cc_final: 0.7262 (pm20) REVERT: O 657 ASN cc_start: 0.6810 (t0) cc_final: 0.6529 (t0) REVERT: O 688 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8015 (tm-30) REVERT: O 692 MET cc_start: 0.7837 (mtm) cc_final: 0.7264 (mtm) REVERT: P 28 LEU cc_start: 0.8658 (tp) cc_final: 0.8104 (mm) REVERT: P 94 MET cc_start: 0.7399 (mmp) cc_final: 0.7121 (mmp) REVERT: P 104 MET cc_start: 0.7772 (mmm) cc_final: 0.7525 (tpp) REVERT: P 167 THR cc_start: 0.9185 (m) cc_final: 0.8615 (p) REVERT: P 180 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7730 (mt-10) REVERT: P 267 GLU cc_start: 0.6910 (mp0) cc_final: 0.6103 (mp0) REVERT: Q 59 TYR cc_start: 0.7418 (t80) cc_final: 0.7024 (t80) REVERT: Q 116 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7057 (mt-10) REVERT: Q 121 GLN cc_start: 0.6399 (mp10) cc_final: 0.5710 (mp10) REVERT: Q 151 GLU cc_start: 0.7646 (tp30) cc_final: 0.6169 (tp30) REVERT: Q 158 ARG cc_start: 0.7382 (mtt-85) cc_final: 0.7175 (ttm110) REVERT: Q 160 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7125 (mm-40) REVERT: Q 173 LYS cc_start: 0.8436 (ptpp) cc_final: 0.7827 (ptpp) REVERT: Q 181 GLU cc_start: 0.7836 (tt0) cc_final: 0.7351 (tt0) REVERT: R 207 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.6972 (pp20) REVERT: R 259 LYS cc_start: 0.9008 (mmtp) cc_final: 0.8665 (mttp) REVERT: R 260 MET cc_start: 0.7851 (tpp) cc_final: 0.7516 (tpp) REVERT: R 313 ASN cc_start: 0.8274 (t0) cc_final: 0.7979 (t0) REVERT: R 316 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8091 (tm-30) REVERT: R 322 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7561 (tm-30) REVERT: R 334 TYR cc_start: 0.8309 (t80) cc_final: 0.8030 (t80) REVERT: R 371 GLU cc_start: 0.7492 (tm-30) cc_final: 0.6889 (tm-30) REVERT: R 433 CYS cc_start: 0.7913 (p) cc_final: 0.7620 (p) REVERT: R 455 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7957 (ttm170) REVERT: R 464 ARG cc_start: 0.7343 (mtm-85) cc_final: 0.7001 (mtm110) REVERT: R 466 ASP cc_start: 0.8759 (p0) cc_final: 0.8504 (p0) REVERT: R 470 ILE cc_start: 0.8938 (mm) cc_final: 0.8618 (pt) REVERT: R 503 GLN cc_start: 0.7544 (pm20) cc_final: 0.6853 (pm20) REVERT: R 522 GLU cc_start: 0.7428 (pm20) cc_final: 0.7185 (pm20) REVERT: R 530 ILE cc_start: 0.8884 (mm) cc_final: 0.8613 (tp) REVERT: R 556 ASN cc_start: 0.8828 (m-40) cc_final: 0.8610 (m-40) REVERT: R 605 ILE cc_start: 0.8778 (mt) cc_final: 0.8365 (pt) REVERT: R 640 LYS cc_start: 0.8695 (tptt) cc_final: 0.8405 (tptm) REVERT: R 679 MET cc_start: 0.4314 (OUTLIER) cc_final: 0.3911 (tmm) REVERT: d 2 ASP cc_start: 0.8393 (t0) cc_final: 0.8075 (t0) REVERT: d 38 ASP cc_start: 0.8092 (m-30) cc_final: 0.7779 (m-30) REVERT: d 43 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7898 (ttp-110) REVERT: d 81 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7028 (mt-10) REVERT: d 102 ARG cc_start: 0.7867 (mtp85) cc_final: 0.6875 (mtp85) REVERT: d 136 GLU cc_start: 0.7990 (tp30) cc_final: 0.7631 (tp30) REVERT: d 170 ASN cc_start: 0.7789 (t0) cc_final: 0.7165 (t0) REVERT: d 180 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7227 (mm-30) REVERT: d 182 ARG cc_start: 0.8508 (tpp80) cc_final: 0.7778 (tpp80) REVERT: d 183 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8393 (ptpp) REVERT: d 220 ASP cc_start: 0.7412 (t0) cc_final: 0.7094 (t0) REVERT: d 230 MET cc_start: 0.7179 (mtp) cc_final: 0.6966 (mtp) REVERT: d 248 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8600 (p) REVERT: d 269 ASN cc_start: 0.8246 (t0) cc_final: 0.7889 (t0) outliers start: 154 outliers final: 117 residues processed: 1243 average time/residue: 0.2645 time to fit residues: 498.5441 Evaluate side-chains 1306 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 1169 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 92 TYR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 331 ASP Chi-restraints excluded: chain G residue 453 THR Chi-restraints excluded: chain G residue 456 LYS Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 157 HIS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain J residue 587 GLU Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain J residue 598 GLU Chi-restraints excluded: chain J residue 654 CYS Chi-restraints excluded: chain c residue 33 MET Chi-restraints excluded: chain c residue 73 THR Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 99 VAL Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain c residue 172 THR Chi-restraints excluded: chain c residue 174 GLU Chi-restraints excluded: chain c residue 241 SER Chi-restraints excluded: chain c residue 248 THR Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 270 MET Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 65 MET Chi-restraints excluded: chain M residue 86 ARG Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 314 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain O residue 433 CYS Chi-restraints excluded: chain O residue 446 VAL Chi-restraints excluded: chain O residue 457 ILE Chi-restraints excluded: chain O residue 540 SER Chi-restraints excluded: chain O residue 647 ILE Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 160 PHE Chi-restraints excluded: chain P residue 172 THR Chi-restraints excluded: chain P residue 178 LEU Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 227 SER Chi-restraints excluded: chain P residue 248 THR Chi-restraints excluded: chain P residue 250 TYR Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 20 TYR Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain Q residue 114 THR Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 156 ASN Chi-restraints excluded: chain Q residue 157 HIS Chi-restraints excluded: chain Q residue 160 GLN Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 238 LYS Chi-restraints excluded: chain R residue 282 ILE Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 455 ARG Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 654 CYS Chi-restraints excluded: chain R residue 677 THR Chi-restraints excluded: chain R residue 679 MET Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 167 THR Chi-restraints excluded: chain d residue 172 THR Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 284 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 234 optimal weight: 0.0870 chunk 99 optimal weight: 0.0870 chunk 336 optimal weight: 0.8980 chunk 389 optimal weight: 1.9990 chunk 340 optimal weight: 0.8980 chunk 277 optimal weight: 0.9990 chunk 276 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 135 optimal weight: 0.1980 overall best weight: 0.2734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN F 109 ASN G 503 GLN G 545 HIS G 547 GLN ** G 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 143 HIS ** I 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 146 GLN c 257 ASN K 220 HIS N 157 HIS ** N 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 347 HIS Q 157 HIS R 342 GLN ** R 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.132098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.111040 restraints weight = 72405.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114882 restraints weight = 34792.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.117460 restraints weight = 21216.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.119133 restraints weight = 14909.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.120290 restraints weight = 11551.744| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34806 Z= 0.148 Angle : 0.758 13.187 47180 Z= 0.382 Chirality : 0.045 0.192 4964 Planarity : 0.006 0.183 6150 Dihedral : 5.030 42.399 4634 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.23 % Favored : 94.70 % Rotamer: Outliers : 3.46 % Allowed : 24.73 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.51 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.13), residues: 4110 helix: 0.30 (0.15), residues: 1147 sheet: -0.97 (0.18), residues: 797 loop : -0.39 (0.14), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 41 TYR 0.029 0.002 TYR N 67 PHE 0.030 0.001 PHE B 213 TRP 0.054 0.002 TRP M 187 HIS 0.008 0.001 HIS F 157 Details of bonding type rmsd covalent geometry : bond 0.00338 (34806) covalent geometry : angle 0.75761 (47180) hydrogen bonds : bond 0.03858 ( 1325) hydrogen bonds : angle 5.52730 ( 3786) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8220 Ramachandran restraints generated. 4110 Oldfield, 0 Emsley, 4110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 1165 time to evaluate : 1.474 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: 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: symmetry clash revert: symmetry clash REVERT: A 7 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.6128 (mptp) REVERT: A 21 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8466 (p) REVERT: B 144 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7725 (mt) REVERT: B 150 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7356 (t0) REVERT: B 192 THR cc_start: 0.8589 (p) cc_final: 0.8372 (p) REVERT: B 215 VAL cc_start: 0.8708 (t) cc_final: 0.8465 (m) REVERT: B 218 LYS cc_start: 0.7908 (mttp) cc_final: 0.7621 (mttp) REVERT: B 226 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7055 (mt-10) REVERT: B 253 ASP cc_start: 0.7796 (t0) cc_final: 0.7401 (t0) REVERT: D 294 TRP cc_start: 0.7778 (t60) cc_final: 0.6702 (t60) REVERT: D 298 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7586 (mm-30) REVERT: D 307 MET cc_start: 0.7140 (tpp) cc_final: 0.6880 (tpp) REVERT: D 323 ARG cc_start: 0.8420 (ttm110) cc_final: 0.8122 (ttm-80) REVERT: E 26 LYS cc_start: 0.7899 (mttm) cc_final: 0.7666 (mttm) REVERT: E 44 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.7267 (ttp-110) REVERT: E 46 LYS cc_start: 0.7690 (tttm) cc_final: 0.7225 (tmtm) REVERT: E 74 MET cc_start: 0.7027 (mmp) cc_final: 0.6154 (mmm) REVERT: E 97 MET cc_start: 0.5455 (mmt) cc_final: 0.4780 (mmt) REVERT: E 113 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8113 (pp) REVERT: E 123 ARG cc_start: 0.6896 (OUTLIER) cc_final: 0.6276 (mmp80) REVERT: E 195 ASN cc_start: 0.7791 (m110) cc_final: 0.7450 (t0) REVERT: F 44 TYR cc_start: 0.7853 (t80) cc_final: 0.7611 (t80) REVERT: F 67 TYR cc_start: 0.7562 (t80) cc_final: 0.6480 (t80) REVERT: F 98 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7195 (mm-40) REVERT: F 116 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6822 (mt-10) REVERT: F 122 ARG cc_start: 0.8063 (mpp80) cc_final: 0.7573 (mtt90) REVERT: F 133 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8734 (p) REVERT: F 142 VAL cc_start: 0.8751 (t) cc_final: 0.7786 (m) REVERT: F 147 GLU cc_start: 0.7464 (tt0) cc_final: 0.6756 (tt0) REVERT: F 156 ASN cc_start: 0.8337 (p0) cc_final: 0.8120 (p0) REVERT: G 251 ILE cc_start: 0.8179 (tt) cc_final: 0.7877 (tp) REVERT: G 257 ASP cc_start: 0.8047 (t70) cc_final: 0.7509 (t70) REVERT: G 276 MET cc_start: 0.6952 (mmm) cc_final: 0.6552 (mmm) REVERT: G 281 GLU cc_start: 0.8089 (pt0) cc_final: 0.7492 (pp20) REVERT: G 284 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7283 (mm-30) REVERT: G 287 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8528 (mmmt) REVERT: G 316 GLU cc_start: 0.8225 (tt0) cc_final: 0.7787 (tt0) REVERT: G 332 GLU cc_start: 0.8200 (tp30) cc_final: 0.7846 (tm-30) REVERT: G 351 ARG cc_start: 0.7390 (ttp-170) cc_final: 0.7107 (ttp-170) REVERT: G 451 ILE cc_start: 0.8281 (mt) cc_final: 0.7905 (mm) REVERT: G 667 TYR cc_start: 0.5915 (m-10) cc_final: 0.5604 (m-10) REVERT: G 688 GLN cc_start: 0.8629 (tp-100) cc_final: 0.7545 (tp40) REVERT: G 692 MET cc_start: 0.7495 (mmp) cc_final: 0.7173 (mmp) REVERT: H 39 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: H 110 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7305 (mm-30) REVERT: H 145 ASP cc_start: 0.7930 (t0) cc_final: 0.7559 (t0) REVERT: H 149 LYS cc_start: 0.8641 (mtpp) cc_final: 0.8424 (mtpp) REVERT: H 171 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7908 (ptm-80) REVERT: I 66 ARG cc_start: 0.7749 (ttm-80) cc_final: 0.7364 (ttm-80) REVERT: I 106 TYR cc_start: 0.8080 (m-80) cc_final: 0.7775 (m-80) REVERT: I 111 ASP cc_start: 0.8012 (m-30) cc_final: 0.7783 (m-30) REVERT: I 116 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7210 (mt-10) REVERT: I 121 GLN cc_start: 0.6073 (mp-120) cc_final: 0.5839 (mp-120) REVERT: I 122 ARG cc_start: 0.7893 (mpp80) cc_final: 0.6604 (mtt90) REVERT: I 136 LYS cc_start: 0.8212 (mttt) cc_final: 0.7947 (mttt) REVERT: I 142 VAL cc_start: 0.8765 (t) cc_final: 0.8500 (p) REVERT: I 153 ILE cc_start: 0.8810 (mp) cc_final: 0.8033 (mt) REVERT: I 158 ARG cc_start: 0.8207 (ttm110) cc_final: 0.7519 (ttm110) REVERT: I 185 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7250 (mt-10) REVERT: J 211 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7731 (mm-40) REVERT: J 216 TYR cc_start: 0.8547 (t80) cc_final: 0.8104 (t80) REVERT: J 237 THR cc_start: 0.8741 (m) cc_final: 0.8534 (p) REVERT: J 256 GLN cc_start: 0.8382 (mt0) cc_final: 0.8094 (mm110) REVERT: J 260 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7104 (tmm) REVERT: J 281 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7357 (mp0) REVERT: J 313 ASN cc_start: 0.8079 (t0) cc_final: 0.7638 (t0) REVERT: J 315 MET cc_start: 0.8666 (mmm) cc_final: 0.8430 (mmp) REVERT: J 322 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: J 438 ARG cc_start: 0.8810 (tpp80) cc_final: 0.8581 (mpp80) REVERT: J 464 ARG cc_start: 0.7385 (mtm-85) cc_final: 0.7032 (mtm-85) REVERT: J 587 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7273 (pt0) REVERT: J 619 GLN cc_start: 0.7179 (pm20) cc_final: 0.6864 (pm20) REVERT: J 620 TYR cc_start: 0.8127 (m-80) cc_final: 0.7781 (m-80) REVERT: c 24 ARG cc_start: 0.8136 (mmt-90) cc_final: 0.7731 (tpp80) REVERT: c 41 PHE cc_start: 0.9232 (m-80) cc_final: 0.8791 (m-80) REVERT: c 45 LEU cc_start: 0.8212 (mp) cc_final: 0.8011 (mt) REVERT: c 145 ASP cc_start: 0.8110 (m-30) cc_final: 0.7725 (m-30) REVERT: c 170 ASN cc_start: 0.7607 (t0) cc_final: 0.7088 (t0) REVERT: c 182 ARG cc_start: 0.8031 (mmm-85) cc_final: 0.7736 (mmm-85) REVERT: c 191 ARG cc_start: 0.7581 (mtp180) cc_final: 0.7315 (mtp180) REVERT: c 258 TYR cc_start: 0.8219 (p90) cc_final: 0.7842 (p90) REVERT: c 262 TYR cc_start: 0.8824 (t80) cc_final: 0.8052 (t80) REVERT: c 269 ASN cc_start: 0.8402 (t0) cc_final: 0.7843 (t0) REVERT: c 270 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7257 (ppp) REVERT: c 271 ASP cc_start: 0.7751 (m-30) cc_final: 0.6813 (m-30) REVERT: C 7 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.6632 (tptt) REVERT: K 153 PHE cc_start: 0.8087 (m-80) cc_final: 0.7871 (m-80) REVERT: K 189 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7615 (mmt90) REVERT: K 210 ASP cc_start: 0.7894 (t0) cc_final: 0.7675 (t0) REVERT: K 253 ASP cc_start: 0.7971 (m-30) cc_final: 0.7112 (t0) REVERT: K 287 LYS cc_start: 0.8420 (mtpt) cc_final: 0.8008 (mttp) REVERT: K 295 ASP cc_start: 0.6880 (t0) cc_final: 0.6637 (t0) REVERT: L 294 TRP cc_start: 0.7921 (t60) cc_final: 0.7018 (t60) REVERT: L 307 MET cc_start: 0.7485 (tpp) cc_final: 0.7141 (tpp) REVERT: L 323 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.7901 (ttm-80) REVERT: M 47 LEU cc_start: 0.7356 (mm) cc_final: 0.6838 (mp) REVERT: M 88 LYS cc_start: 0.8172 (mmmm) cc_final: 0.7775 (tppp) REVERT: M 92 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7700 (t80) REVERT: M 95 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7615 (mt-10) REVERT: M 96 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8385 (mm) REVERT: M 97 MET cc_start: 0.5697 (mmt) cc_final: 0.5370 (mmt) REVERT: M 158 LYS cc_start: 0.8354 (mttt) cc_final: 0.7992 (mttt) REVERT: M 193 MET cc_start: 0.7389 (mmm) cc_final: 0.6928 (tmm) REVERT: N 91 GLU cc_start: 0.7112 (mp0) cc_final: 0.6838 (mp0) REVERT: N 98 GLN cc_start: 0.8217 (mt0) cc_final: 0.7732 (mt0) REVERT: N 109 ASN cc_start: 0.8603 (p0) cc_final: 0.8120 (p0) REVERT: N 116 GLU cc_start: 0.7536 (mm-30) cc_final: 0.7090 (mm-30) REVERT: N 136 LYS cc_start: 0.8543 (mttt) cc_final: 0.8278 (mtmm) REVERT: N 185 GLU cc_start: 0.7372 (tt0) cc_final: 0.6839 (tt0) REVERT: N 196 GLU cc_start: 0.8226 (mp0) cc_final: 0.7932 (mp0) REVERT: O 252 GLU cc_start: 0.7702 (mp0) cc_final: 0.7280 (mp0) REVERT: O 281 GLU cc_start: 0.8492 (pt0) cc_final: 0.8204 (pt0) REVERT: O 284 GLU cc_start: 0.7922 (tp30) cc_final: 0.7324 (tp30) REVERT: O 316 GLU cc_start: 0.8342 (tt0) cc_final: 0.8081 (tt0) REVERT: O 350 GLN cc_start: 0.8363 (tm-30) cc_final: 0.7802 (tm-30) REVERT: O 371 GLU cc_start: 0.7132 (tp30) cc_final: 0.6619 (tp30) REVERT: O 438 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7918 (mtp85) REVERT: O 502 TYR cc_start: 0.6122 (p90) cc_final: 0.4772 (p90) REVERT: O 643 GLU cc_start: 0.7408 (pm20) cc_final: 0.7010 (pm20) REVERT: O 667 TYR cc_start: 0.5617 (m-80) cc_final: 0.5308 (m-80) REVERT: O 688 GLN cc_start: 0.8454 (tm-30) cc_final: 0.7876 (tm-30) REVERT: O 692 MET cc_start: 0.7786 (mtm) cc_final: 0.7112 (mtm) REVERT: P 28 LEU cc_start: 0.8579 (tp) cc_final: 0.8017 (mm) REVERT: P 43 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7184 (mtm-85) REVERT: P 67 GLN cc_start: 0.8333 (mm-40) cc_final: 0.6116 (mm-40) REVERT: P 94 MET cc_start: 0.7319 (mmp) cc_final: 0.7059 (mmp) REVERT: P 104 MET cc_start: 0.7800 (mmm) cc_final: 0.7488 (tpp) REVERT: P 156 ARG cc_start: 0.7604 (tpt90) cc_final: 0.7250 (tpt90) REVERT: P 180 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7722 (mt-10) REVERT: P 267 GLU cc_start: 0.6906 (mp0) cc_final: 0.6155 (mp0) REVERT: Q 59 TYR cc_start: 0.7365 (t80) cc_final: 0.7001 (t80) REVERT: Q 116 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7019 (mt-10) REVERT: Q 121 GLN cc_start: 0.6367 (mp10) cc_final: 0.5714 (mp10) REVERT: Q 173 LYS cc_start: 0.8414 (ptpp) cc_final: 0.7734 (ptpp) REVERT: Q 181 GLU cc_start: 0.7715 (tt0) cc_final: 0.7242 (tt0) REVERT: R 207 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.6646 (mp0) REVERT: R 259 LYS cc_start: 0.8996 (mmtp) cc_final: 0.8570 (mttp) REVERT: R 284 GLU cc_start: 0.7649 (pm20) cc_final: 0.7381 (pm20) REVERT: R 313 ASN cc_start: 0.8257 (t0) cc_final: 0.7580 (t0) REVERT: R 322 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7505 (tm-30) REVERT: R 371 GLU cc_start: 0.7476 (tm-30) cc_final: 0.6859 (tm-30) REVERT: R 433 CYS cc_start: 0.7911 (p) cc_final: 0.7685 (p) REVERT: R 438 ARG cc_start: 0.8784 (tpp80) cc_final: 0.8227 (mtt90) REVERT: R 466 ASP cc_start: 0.8710 (p0) cc_final: 0.8441 (p0) REVERT: R 470 ILE cc_start: 0.8896 (mm) cc_final: 0.8626 (pt) REVERT: R 503 GLN cc_start: 0.7503 (pm20) cc_final: 0.6794 (pm20) REVERT: R 522 GLU cc_start: 0.7451 (pm20) cc_final: 0.7114 (pm20) REVERT: R 530 ILE cc_start: 0.8876 (mm) cc_final: 0.8602 (tp) REVERT: R 556 ASN cc_start: 0.8816 (m-40) cc_final: 0.8543 (m-40) REVERT: R 616 LEU cc_start: 0.8694 (mm) cc_final: 0.8486 (mt) REVERT: R 619 GLN cc_start: 0.8122 (tp-100) cc_final: 0.7665 (tp-100) REVERT: R 640 LYS cc_start: 0.8640 (tptt) cc_final: 0.8349 (tptm) REVERT: R 679 MET cc_start: 0.4270 (OUTLIER) cc_final: 0.3918 (tmm) REVERT: d 2 ASP cc_start: 0.8384 (t0) cc_final: 0.7975 (t0) REVERT: d 33 MET cc_start: 0.7752 (tpp) cc_final: 0.7368 (tpp) REVERT: d 38 ASP cc_start: 0.8062 (m-30) cc_final: 0.7754 (m-30) REVERT: d 43 ARG cc_start: 0.8125 (ttp80) cc_final: 0.7437 (ttp80) REVERT: d 81 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7004 (mt-10) REVERT: d 167 THR cc_start: 0.6805 (m) cc_final: 0.6369 (p) REVERT: d 170 ASN cc_start: 0.7787 (t0) cc_final: 0.7142 (t0) REVERT: d 180 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7153 (mm-30) REVERT: d 182 ARG cc_start: 0.8439 (tpp80) cc_final: 0.8164 (tpp80) REVERT: d 183 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8365 (ptpp) REVERT: d 220 ASP cc_start: 0.7438 (t0) cc_final: 0.7082 (t0) REVERT: d 248 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8528 (p) REVERT: d 269 ASN cc_start: 0.8222 (t0) cc_final: 0.7826 (t0) outliers start: 126 outliers final: 96 residues processed: 1209 average time/residue: 0.2578 time to fit residues: 473.3581 Evaluate side-chains 1260 residues out of total 3644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 1146 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 250 LYS Chi-restraints excluded: chain B residue 272 ILE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 168 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 151 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 199 GLU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 453 THR Chi-restraints excluded: chain G residue 456 LYS Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain G residue 545 HIS Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 171 ARG Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 255 THR Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 267 GLU Chi-restraints excluded: chain I residue 38 LEU Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain I residue 132 GLU Chi-restraints excluded: chain I residue 157 HIS Chi-restraints excluded: chain I residue 180 CYS Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain J residue 260 MET Chi-restraints excluded: chain J residue 322 GLU Chi-restraints excluded: chain J residue 588 VAL Chi-restraints excluded: chain J residue 598 GLU Chi-restraints excluded: chain c residue 84 LEU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 168 HIS Chi-restraints excluded: chain c residue 172 THR Chi-restraints excluded: chain c residue 174 GLU Chi-restraints excluded: chain c residue 241 SER Chi-restraints excluded: chain c residue 248 THR Chi-restraints excluded: chain c residue 251 HIS Chi-restraints excluded: chain c residue 270 MET Chi-restraints excluded: chain C residue 7 LYS Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 192 THR Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 322 GLU Chi-restraints excluded: chain M residue 65 MET Chi-restraints excluded: chain M residue 92 TYR Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 130 ASN Chi-restraints excluded: chain M residue 153 ILE Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 168 THR Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain N residue 104 VAL Chi-restraints excluded: chain N residue 147 GLU Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain O residue 228 LEU Chi-restraints excluded: chain O residue 290 PHE Chi-restraints excluded: chain O residue 314 VAL Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain O residue 433 CYS Chi-restraints excluded: chain O residue 446 VAL Chi-restraints excluded: chain O residue 457 ILE Chi-restraints excluded: chain O residue 647 ILE Chi-restraints excluded: chain P residue 75 TYR Chi-restraints excluded: chain P residue 90 GLU Chi-restraints excluded: chain P residue 172 THR Chi-restraints excluded: chain P residue 181 VAL Chi-restraints excluded: chain P residue 227 SER Chi-restraints excluded: chain P residue 248 THR Chi-restraints excluded: chain P residue 250 TYR Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain Q residue 44 TYR Chi-restraints excluded: chain Q residue 114 THR Chi-restraints excluded: chain Q residue 133 THR Chi-restraints excluded: chain Q residue 156 ASN Chi-restraints excluded: chain Q residue 157 HIS Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain R residue 207 GLU Chi-restraints excluded: chain R residue 287 LYS Chi-restraints excluded: chain R residue 526 ASP Chi-restraints excluded: chain R residue 641 LYS Chi-restraints excluded: chain R residue 677 THR Chi-restraints excluded: chain R residue 679 MET Chi-restraints excluded: chain d residue 23 ASP Chi-restraints excluded: chain d residue 94 MET Chi-restraints excluded: chain d residue 138 THR Chi-restraints excluded: chain d residue 159 LEU Chi-restraints excluded: chain d residue 174 GLU Chi-restraints excluded: chain d residue 248 THR Chi-restraints excluded: chain d residue 250 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 87 optimal weight: 0.6980 chunk 258 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 309 optimal weight: 0.2980 chunk 262 optimal weight: 0.0980 chunk 77 optimal weight: 0.2980 chunk 271 optimal weight: 0.6980 chunk 308 optimal weight: 0.0980 chunk 299 optimal weight: 0.0070 chunk 123 optimal weight: 0.8980 chunk 373 optimal weight: 3.9990 overall best weight: 0.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 HIS ** G 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 79 GLN I 143 HIS ** c 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 234 ASN ** N 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 286 GLN O 347 HIS ** Q 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 165 ASN R 342 GLN ** R 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 229 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.132702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.111855 restraints weight = 72478.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.115724 restraints weight = 34691.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.118223 restraints weight = 21023.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.120008 restraints weight = 14801.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.120958 restraints weight = 11317.281| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34806 Z= 0.141 Angle : 0.752 13.114 47180 Z= 0.378 Chirality : 0.045 0.193 4964 Planarity : 0.005 0.132 6150 Dihedral : 4.968 49.416 4634 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.47 % Favored : 94.45 % Rotamer: Outliers : 3.43 % Allowed : 25.36 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.54 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.13), residues: 4110 helix: 0.35 (0.15), residues: 1141 sheet: -0.92 (0.17), residues: 831 loop : -0.42 (0.14), residues: 2138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 232 TYR 0.023 0.001 TYR E 160 PHE 0.028 0.001 PHE B 213 TRP 0.056 0.002 TRP M 191 HIS 0.036 0.001 HIS G 545 Details of bonding type rmsd covalent geometry : bond 0.00320 (34806) covalent geometry : angle 0.75237 (47180) hydrogen bonds : bond 0.03749 ( 1325) hydrogen bonds : angle 5.47189 ( 3786) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9316.40 seconds wall clock time: 160 minutes 38.93 seconds (9638.93 seconds total)