Starting phenix.real_space_refine on Mon Aug 10 02:57:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10eh_75107/08_2026/10eh_75107.cif Found real_map, /net/cci-nas-00/data/ceres_data/10eh_75107/08_2026/10eh_75107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10eh_75107/08_2026/10eh_75107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10eh_75107/08_2026/10eh_75107.map" model { file = "/net/cci-nas-00/data/ceres_data/10eh_75107/08_2026/10eh_75107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10eh_75107/08_2026/10eh_75107.cif" } resolution = 3.5 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 88 5.49 5 S 172 5.16 5 C 25662 2.51 5 N 6684 2.21 5 O 7542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40149 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 4123 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 33, 'TRANS': 459} Chain breaks: 3 Chain: "B" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4844 Classifications: {'peptide': 586} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 566} Chain breaks: 1 Chain: "C" Number of atoms: 4828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4828 Classifications: {'peptide': 585} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 564} Chain breaks: 1 Chain: "D" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3568 Classifications: {'peptide': 423} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 410} Chain breaks: 2 Chain: "E" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1272 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 148} Chain breaks: 1 Chain: "F" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 912 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "G" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 892 Classifications: {'DNA': 44} Link IDs: {'rna3p': 43} Chain: "H" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 505 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "I" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 478 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain: "J" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 489 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "a" Number of atoms: 4128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4128 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 33, 'TRANS': 462} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "b" Number of atoms: 4607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4607 Classifications: {'peptide': 554} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 535} Chain breaks: 2 Chain: "c" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4662 Classifications: {'peptide': 564} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 544} Chain breaks: 2 Chain: "d" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3568 Classifications: {'peptide': 423} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 410} Chain breaks: 2 Chain: "e" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1272 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 148} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9038 SG CYS C 14 81.743 65.807 98.883 1.00119.88 S ATOM 9165 SG CYS C 30 80.196 68.884 98.396 1.00129.74 S ATOM 9183 SG CYS C 33 83.040 68.670 101.002 1.00137.47 S ATOM 9256 SG CYS C 42 83.981 68.460 97.318 1.00155.16 S Time building chain proxies: 8.49, per 1000 atoms: 0.21 Number of scatterers: 40149 At special positions: 0 Unit cell: (118.77, 124.12, 276.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 172 16.00 P 88 15.00 O 7542 8.00 N 6684 7.00 C 25662 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 17 " - pdb=" SG CYS B 42 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 33 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.92 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 14 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 30 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 33 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 42 " Number of angles added : 6 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8980 Finding SS restraints... Secondary structure from input PDB file: 229 helices and 19 sheets defined 64.0% alpha, 5.1% beta 27 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 4.57 Creating SS restraints... Processing helix chain 'A' and resid 28 through 36 removed outlier: 4.163A pdb=" N GLU A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 59 Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 111 through 140 removed outlier: 4.056A pdb=" N HIS A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A 140 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 174 Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 207 through 225 removed outlier: 3.917A pdb=" N LYS A 211 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 334 through 350 Processing helix chain 'A' and resid 355 through 360 removed outlier: 3.544A pdb=" N PHE A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 355 through 360' Processing helix chain 'A' and resid 371 through 379 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 400 through 408 removed outlier: 3.628A pdb=" N ASN A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 4.193A pdb=" N GLN A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 430 through 435' Processing helix chain 'A' and resid 436 through 447 removed outlier: 4.075A pdb=" N ASP A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A 446 " --> pdb=" O TYR A 442 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N TYR A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 451 through 479 removed outlier: 4.161A pdb=" N PHE A 457 " --> pdb=" O ASN A 453 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 460 " --> pdb=" O ASP A 456 " (cutoff:3.500A) Proline residue: A 473 - end of helix Processing helix chain 'A' and resid 482 through 486 Processing helix chain 'A' and resid 487 through 491 Processing helix chain 'A' and resid 492 through 503 removed outlier: 3.727A pdb=" N THR A 503 " --> pdb=" O PHE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 526 removed outlier: 4.104A pdb=" N ASN A 526 " --> pdb=" O LYS A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 532 Processing helix chain 'B' and resid 15 through 20 removed outlier: 4.426A pdb=" N ARG B 20 " --> pdb=" O VAL B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 73 removed outlier: 3.593A pdb=" N GLN B 66 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 106 Processing helix chain 'B' and resid 107 through 121 removed outlier: 3.569A pdb=" N SER B 111 " --> pdb=" O GLN B 107 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 131 Processing helix chain 'B' and resid 132 through 148 removed outlier: 3.605A pdb=" N LEU B 136 " --> pdb=" O ASP B 132 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU B 141 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 148 " --> pdb=" O TRP B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 173 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 185 through 193 Processing helix chain 'B' and resid 199 through 223 removed outlier: 4.236A pdb=" N GLY B 203 " --> pdb=" O ASN B 199 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLN B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 206 " --> pdb=" O ASP B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 230 through 241 removed outlier: 3.872A pdb=" N VAL B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 Processing helix chain 'B' and resid 249 through 267 removed outlier: 3.909A pdb=" N PHE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 303 removed outlier: 3.571A pdb=" N ARG B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.554A pdb=" N ARG B 336 " --> pdb=" O ASP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 366 through 387 Processing helix chain 'B' and resid 393 through 422 removed outlier: 3.788A pdb=" N ARG B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 444 Processing helix chain 'B' and resid 445 through 446 No H-bonds generated for 'chain 'B' and resid 445 through 446' Processing helix chain 'B' and resid 447 through 455 removed outlier: 5.970A pdb=" N PHE B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 477 removed outlier: 3.845A pdb=" N MET B 460 " --> pdb=" O HIS B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 495 Processing helix chain 'B' and resid 501 through 524 removed outlier: 3.846A pdb=" N ASP B 505 " --> pdb=" O GLY B 501 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU B 519 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 520 " --> pdb=" O LYS B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 552 Processing helix chain 'B' and resid 554 through 562 Processing helix chain 'B' and resid 590 through 601 removed outlier: 3.912A pdb=" N VAL B 594 " --> pdb=" O PHE B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 607 Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 30 through 36 Processing helix chain 'C' and resid 40 through 44 removed outlier: 4.004A pdb=" N MET C 43 " --> pdb=" O SER C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 73 removed outlier: 3.900A pdb=" N GLN C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 106 removed outlier: 3.951A pdb=" N THR C 96 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 122 Processing helix chain 'C' and resid 122 through 127 removed outlier: 3.592A pdb=" N TYR C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 147 removed outlier: 3.560A pdb=" N TYR C 137 " --> pdb=" O ILE C 133 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 174 Processing helix chain 'C' and resid 175 through 183 Processing helix chain 'C' and resid 185 through 193 removed outlier: 4.011A pdb=" N GLU C 190 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR C 191 " --> pdb=" O PRO C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 202 Processing helix chain 'C' and resid 203 through 224 Processing helix chain 'C' and resid 230 through 241 removed outlier: 3.963A pdb=" N VAL C 234 " --> pdb=" O ASP C 230 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE C 239 " --> pdb=" O GLN C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 265 Processing helix chain 'C' and resid 279 through 302 Processing helix chain 'C' and resid 319 through 329 removed outlier: 4.382A pdb=" N ALA C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TYR C 325 " --> pdb=" O GLN C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 357 removed outlier: 3.879A pdb=" N LEU C 344 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP C 346 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 386 removed outlier: 3.845A pdb=" N ALA C 372 " --> pdb=" O LYS C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 422 removed outlier: 3.559A pdb=" N ARG C 397 " --> pdb=" O SER C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 445 removed outlier: 4.029A pdb=" N ASN C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 456 removed outlier: 3.530A pdb=" N ASN C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS C 456 " --> pdb=" O PHE C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 477 removed outlier: 4.004A pdb=" N ILE C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG C 465 " --> pdb=" O GLN C 461 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 493 removed outlier: 4.226A pdb=" N GLU C 491 " --> pdb=" O VAL C 487 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 524 Processing helix chain 'C' and resid 535 through 553 removed outlier: 4.027A pdb=" N ILE C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 563 Processing helix chain 'C' and resid 589 through 601 removed outlier: 3.927A pdb=" N ILE C 593 " --> pdb=" O ASP C 589 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 594 " --> pdb=" O PHE C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 606 removed outlier: 3.660A pdb=" N ASP C 605 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 12 removed outlier: 3.638A pdb=" N LEU D 12 " --> pdb=" O ARG D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 25 Processing helix chain 'D' and resid 35 through 41 removed outlier: 3.641A pdb=" N LYS D 41 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 66 removed outlier: 3.660A pdb=" N LYS D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 69 No H-bonds generated for 'chain 'D' and resid 67 through 69' Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 76 through 78 No H-bonds generated for 'chain 'D' and resid 76 through 78' Processing helix chain 'D' and resid 80 through 91 Processing helix chain 'D' and resid 97 through 110 Processing helix chain 'D' and resid 143 through 151 removed outlier: 3.621A pdb=" N LYS D 149 " --> pdb=" O LYS D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 163 removed outlier: 3.826A pdb=" N LEU D 162 " --> pdb=" O ASP D 158 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 158 through 163' Processing helix chain 'D' and resid 176 through 191 removed outlier: 3.680A pdb=" N ASP D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU D 188 " --> pdb=" O LEU D 184 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLN D 189 " --> pdb=" O SER D 185 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'D' and resid 280 through 288 removed outlier: 3.788A pdb=" N LEU D 286 " --> pdb=" O LYS D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 309 removed outlier: 3.642A pdb=" N ARG D 308 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 381 removed outlier: 4.075A pdb=" N ASN D 375 " --> pdb=" O ASN D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 391 Processing helix chain 'D' and resid 397 through 403 removed outlier: 3.775A pdb=" N LYS D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 435 removed outlier: 3.586A pdb=" N SER D 433 " --> pdb=" O ILE D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 460 Processing helix chain 'E' and resid 20 through 24 Processing helix chain 'E' and resid 26 through 35 removed outlier: 3.743A pdb=" N ASP E 35 " --> pdb=" O ASN E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 127 through 142 Processing helix chain 'E' and resid 143 through 160 Processing helix chain 'E' and resid 162 through 169 removed outlier: 3.724A pdb=" N ILE E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 188 Processing helix chain 'H' and resid 575 through 606 removed outlier: 4.359A pdb=" N GLN H 579 " --> pdb=" O GLU H 575 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN H 580 " --> pdb=" O LEU H 576 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER H 591 " --> pdb=" O PHE H 587 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASN H 592 " --> pdb=" O GLN H 588 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN H 594 " --> pdb=" O LEU H 590 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE H 595 " --> pdb=" O SER H 591 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS H 602 " --> pdb=" O SER H 598 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS H 606 " --> pdb=" O LYS H 602 " (cutoff:3.500A) Processing helix chain 'H' and resid 610 through 618 removed outlier: 3.522A pdb=" N TYR H 616 " --> pdb=" O SER H 612 " (cutoff:3.500A) Processing helix chain 'H' and resid 618 through 629 removed outlier: 4.100A pdb=" N LYS H 625 " --> pdb=" O LEU H 621 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ILE H 626 " --> pdb=" O ASN H 622 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR H 627 " --> pdb=" O LEU H 623 " (cutoff:3.500A) Processing helix chain 'I' and resid 581 through 583 No H-bonds generated for 'chain 'I' and resid 581 through 583' Processing helix chain 'I' and resid 584 through 606 removed outlier: 4.257A pdb=" N GLN I 588 " --> pdb=" O TYR I 584 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASN I 592 " --> pdb=" O GLN I 588 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE I 593 " --> pdb=" O THR I 589 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL I 599 " --> pdb=" O ILE I 595 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS I 606 " --> pdb=" O LYS I 602 " (cutoff:3.500A) Processing helix chain 'I' and resid 610 through 634 removed outlier: 3.709A pdb=" N TYR I 616 " --> pdb=" O SER I 612 " (cutoff:3.500A) Processing helix chain 'J' and resid 578 through 607 removed outlier: 4.503A pdb=" N PHE J 582 " --> pdb=" O LYS J 578 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE J 587 " --> pdb=" O GLU J 583 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN J 592 " --> pdb=" O GLN J 588 " (cutoff:3.500A) Processing helix chain 'J' and resid 610 through 632 removed outlier: 3.592A pdb=" N GLY J 615 " --> pdb=" O LYS J 611 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR J 616 " --> pdb=" O SER J 612 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU J 618 " --> pdb=" O ARG J 614 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE J 626 " --> pdb=" O ASN J 622 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR J 627 " --> pdb=" O LEU J 623 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU J 628 " --> pdb=" O PHE J 624 " (cutoff:3.500A) Processing helix chain 'a' and resid 27 through 35 Processing helix chain 'a' and resid 38 through 59 Processing helix chain 'a' and resid 81 through 93 Processing helix chain 'a' and resid 115 through 132 removed outlier: 4.402A pdb=" N ILE a 119 " --> pdb=" O ASN a 115 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA a 120 " --> pdb=" O SER a 116 " (cutoff:3.500A) Processing helix chain 'a' and resid 133 through 137 removed outlier: 3.577A pdb=" N CYS a 136 " --> pdb=" O SER a 133 " (cutoff:3.500A) Processing helix chain 'a' and resid 147 through 175 removed outlier: 4.184A pdb=" N LEU a 151 " --> pdb=" O ASP a 147 " (cutoff:3.500A) Processing helix chain 'a' and resid 177 through 182 removed outlier: 3.678A pdb=" N LEU a 181 " --> pdb=" O ASN a 177 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N CYS a 182 " --> pdb=" O THR a 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 177 through 182' Processing helix chain 'a' and resid 183 through 194 removed outlier: 3.620A pdb=" N ASN a 194 " --> pdb=" O LEU a 190 " (cutoff:3.500A) Processing helix chain 'a' and resid 207 through 224 removed outlier: 3.534A pdb=" N LYS a 211 " --> pdb=" O THR a 207 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP a 217 " --> pdb=" O ARG a 213 " (cutoff:3.500A) Processing helix chain 'a' and resid 227 through 232 Processing helix chain 'a' and resid 281 through 296 Processing helix chain 'a' and resid 334 through 349 Processing helix chain 'a' and resid 355 through 360 removed outlier: 3.532A pdb=" N ASN a 360 " --> pdb=" O ARG a 356 " (cutoff:3.500A) Processing helix chain 'a' and resid 371 through 378 Processing helix chain 'a' and resid 395 through 399 Processing helix chain 'a' and resid 400 through 406 Processing helix chain 'a' and resid 407 through 409 No H-bonds generated for 'chain 'a' and resid 407 through 409' Processing helix chain 'a' and resid 428 through 432 Processing helix chain 'a' and resid 437 through 445 removed outlier: 4.090A pdb=" N HIS a 445 " --> pdb=" O GLU a 441 " (cutoff:3.500A) Processing helix chain 'a' and resid 451 through 479 Proline residue: a 473 - end of helix Processing helix chain 'a' and resid 493 through 504 Processing helix chain 'a' and resid 519 through 523 removed outlier: 4.052A pdb=" N LYS a 522 " --> pdb=" O GLY a 519 " (cutoff:3.500A) Processing helix chain 'a' and resid 526 through 532 Processing helix chain 'b' and resid 57 through 72 removed outlier: 3.800A pdb=" N GLN b 66 " --> pdb=" O LEU b 62 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN b 67 " --> pdb=" O LEU b 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 92 through 106 removed outlier: 4.264A pdb=" N THR b 96 " --> pdb=" O LEU b 92 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU b 106 " --> pdb=" O TRP b 102 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 122 Processing helix chain 'b' and resid 122 through 127 removed outlier: 3.533A pdb=" N TYR b 126 " --> pdb=" O LEU b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 132 through 147 removed outlier: 3.597A pdb=" N LEU b 136 " --> pdb=" O ASP b 132 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU b 138 " --> pdb=" O SER b 134 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG b 139 " --> pdb=" O GLU b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 153 through 173 Processing helix chain 'b' and resid 175 through 183 removed outlier: 3.670A pdb=" N GLU b 181 " --> pdb=" O GLU b 177 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE b 182 " --> pdb=" O LYS b 178 " (cutoff:3.500A) Processing helix chain 'b' and resid 185 through 193 Processing helix chain 'b' and resid 203 through 223 removed outlier: 3.628A pdb=" N VAL b 207 " --> pdb=" O GLY b 203 " (cutoff:3.500A) Processing helix chain 'b' and resid 230 through 243 removed outlier: 3.833A pdb=" N VAL b 234 " --> pdb=" O ASP b 230 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR b 243 " --> pdb=" O ILE b 239 " (cutoff:3.500A) Processing helix chain 'b' and resid 244 through 249 removed outlier: 3.572A pdb=" N ASP b 248 " --> pdb=" O THR b 244 " (cutoff:3.500A) Processing helix chain 'b' and resid 249 through 268 removed outlier: 3.502A pdb=" N HIS b 268 " --> pdb=" O PHE b 264 " (cutoff:3.500A) Processing helix chain 'b' and resid 279 through 303 removed outlier: 3.521A pdb=" N ILE b 284 " --> pdb=" O PRO b 280 " (cutoff:3.500A) Processing helix chain 'b' and resid 312 through 316 removed outlier: 3.733A pdb=" N VAL b 316 " --> pdb=" O HIS b 313 " (cutoff:3.500A) Processing helix chain 'b' and resid 322 through 328 removed outlier: 4.405A pdb=" N ASP b 328 " --> pdb=" O ALA b 324 " (cutoff:3.500A) Processing helix chain 'b' and resid 333 through 337 removed outlier: 3.629A pdb=" N ARG b 336 " --> pdb=" O ASP b 333 " (cutoff:3.500A) Processing helix chain 'b' and resid 340 through 357 Processing helix chain 'b' and resid 366 through 387 Processing helix chain 'b' and resid 393 through 422 removed outlier: 3.681A pdb=" N ARG b 397 " --> pdb=" O SER b 393 " (cutoff:3.500A) Processing helix chain 'b' and resid 426 through 445 removed outlier: 3.815A pdb=" N ASN b 445 " --> pdb=" O LEU b 441 " (cutoff:3.500A) Processing helix chain 'b' and resid 450 through 455 Processing helix chain 'b' and resid 456 through 475 removed outlier: 3.505A pdb=" N MET b 460 " --> pdb=" O HIS b 456 " (cutoff:3.500A) Processing helix chain 'b' and resid 479 through 496 Processing helix chain 'b' and resid 501 through 524 Processing helix chain 'b' and resid 535 through 552 removed outlier: 3.516A pdb=" N LYS b 539 " --> pdb=" O HIS b 535 " (cutoff:3.500A) Processing helix chain 'b' and resid 554 through 561 removed outlier: 3.593A pdb=" N LEU b 558 " --> pdb=" O GLU b 554 " (cutoff:3.500A) Processing helix chain 'b' and resid 590 through 601 Processing helix chain 'c' and resid 14 through 20 Processing helix chain 'c' and resid 30 through 36 Processing helix chain 'c' and resid 38 through 46 removed outlier: 3.692A pdb=" N CYS c 42 " --> pdb=" O GLN c 38 " (cutoff:3.500A) Processing helix chain 'c' and resid 57 through 73 removed outlier: 3.656A pdb=" N GLN c 66 " --> pdb=" O LEU c 62 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN c 67 " --> pdb=" O LEU c 63 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 106 Processing helix chain 'c' and resid 107 through 122 Processing helix chain 'c' and resid 122 through 130 removed outlier: 3.587A pdb=" N TYR c 126 " --> pdb=" O LEU c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 133 through 146 Processing helix chain 'c' and resid 153 through 173 removed outlier: 3.526A pdb=" N TYR c 173 " --> pdb=" O MET c 169 " (cutoff:3.500A) Processing helix chain 'c' and resid 175 through 181 Processing helix chain 'c' and resid 185 through 193 Processing helix chain 'c' and resid 203 through 223 Processing helix chain 'c' and resid 224 through 228 Processing helix chain 'c' and resid 230 through 243 removed outlier: 3.884A pdb=" N VAL c 234 " --> pdb=" O ASP c 230 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR c 243 " --> pdb=" O ILE c 239 " (cutoff:3.500A) Processing helix chain 'c' and resid 244 through 249 removed outlier: 3.807A pdb=" N ASP c 248 " --> pdb=" O THR c 244 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU c 249 " --> pdb=" O PHE c 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 244 through 249' Processing helix chain 'c' and resid 249 through 267 removed outlier: 3.760A pdb=" N PHE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) Processing helix chain 'c' and resid 279 through 303 Processing helix chain 'c' and resid 341 through 357 removed outlier: 3.863A pdb=" N TYR c 345 " --> pdb=" O THR c 341 " (cutoff:3.500A) Processing helix chain 'c' and resid 366 through 385 removed outlier: 3.533A pdb=" N TYR c 382 " --> pdb=" O ASP c 378 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS c 383 " --> pdb=" O ILE c 379 " (cutoff:3.500A) Processing helix chain 'c' and resid 393 through 422 removed outlier: 3.545A pdb=" N ARG c 397 " --> pdb=" O SER c 393 " (cutoff:3.500A) Processing helix chain 'c' and resid 426 through 444 Processing helix chain 'c' and resid 445 through 446 No H-bonds generated for 'chain 'c' and resid 445 through 446' Processing helix chain 'c' and resid 447 through 455 removed outlier: 6.015A pdb=" N PHE c 452 " --> pdb=" O LYS c 449 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE c 453 " --> pdb=" O SER c 450 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG c 455 " --> pdb=" O PHE c 452 " (cutoff:3.500A) Processing helix chain 'c' and resid 456 through 477 removed outlier: 3.648A pdb=" N MET c 460 " --> pdb=" O HIS c 456 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE c 476 " --> pdb=" O PHE c 472 " (cutoff:3.500A) Processing helix chain 'c' and resid 481 through 496 removed outlier: 3.574A pdb=" N ALA c 494 " --> pdb=" O THR c 490 " (cutoff:3.500A) Processing helix chain 'c' and resid 497 through 500 Processing helix chain 'c' and resid 501 through 524 removed outlier: 3.912A pdb=" N ASP c 505 " --> pdb=" O GLY c 501 " (cutoff:3.500A) Processing helix chain 'c' and resid 535 through 553 Processing helix chain 'c' and resid 554 through 563 Processing helix chain 'c' and resid 589 through 601 removed outlier: 4.212A pdb=" N VAL c 594 " --> pdb=" O PHE c 590 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN c 598 " --> pdb=" O VAL c 594 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER c 599 " --> pdb=" O GLU c 595 " (cutoff:3.500A) Processing helix chain 'c' and resid 603 through 607 Processing helix chain 'd' and resid 7 through 12 Processing helix chain 'd' and resid 35 through 41 Processing helix chain 'd' and resid 58 through 66 Processing helix chain 'd' and resid 66 through 75 removed outlier: 3.892A pdb=" N PHE d 70 " --> pdb=" O MET d 66 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR d 72 " --> pdb=" O PRO d 68 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N TYR d 73 " --> pdb=" O VAL d 69 " (cutoff:3.500A) Processing helix chain 'd' and resid 80 through 95 removed outlier: 3.580A pdb=" N ILE d 84 " --> pdb=" O SER d 80 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU d 89 " --> pdb=" O GLU d 85 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR d 90 " --> pdb=" O LYS d 86 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE d 92 " --> pdb=" O LEU d 88 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TRP d 93 " --> pdb=" O GLU d 89 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG d 95 " --> pdb=" O ALA d 91 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 110 removed outlier: 3.512A pdb=" N ASP d 102 " --> pdb=" O CYS d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 143 through 151 Processing helix chain 'd' and resid 162 through 166 removed outlier: 3.540A pdb=" N SER d 166 " --> pdb=" O LEU d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 176 through 189 Processing helix chain 'd' and resid 190 through 194 removed outlier: 5.726A pdb=" N PHE d 193 " --> pdb=" O LYS d 190 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA d 194 " --> pdb=" O ASP d 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 190 through 194' Processing helix chain 'd' and resid 257 through 266 removed outlier: 3.737A pdb=" N ILE d 261 " --> pdb=" O SER d 257 " (cutoff:3.500A) Processing helix chain 'd' and resid 267 through 270 Processing helix chain 'd' and resid 281 through 288 Processing helix chain 'd' and resid 302 through 308 removed outlier: 3.612A pdb=" N ARG d 307 " --> pdb=" O TYR d 303 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG d 308 " --> pdb=" O ILE d 304 " (cutoff:3.500A) Processing helix chain 'd' and resid 371 through 381 Processing helix chain 'd' and resid 383 through 391 Processing helix chain 'd' and resid 399 through 404 Processing helix chain 'd' and resid 419 through 435 Processing helix chain 'd' and resid 456 through 461 Processing helix chain 'e' and resid 20 through 24 Processing helix chain 'e' and resid 26 through 34 Processing helix chain 'e' and resid 83 through 97 removed outlier: 3.593A pdb=" N LYS e 89 " --> pdb=" O SER e 85 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 114 Processing helix chain 'e' and resid 117 through 124 Processing helix chain 'e' and resid 127 through 142 Processing helix chain 'e' and resid 143 through 160 removed outlier: 3.526A pdb=" N MET e 157 " --> pdb=" O VAL e 153 " (cutoff:3.500A) Processing helix chain 'e' and resid 162 through 169 removed outlier: 3.834A pdb=" N ARG e 168 " --> pdb=" O GLU e 164 " (cutoff:3.500A) Processing helix chain 'e' and resid 170 through 172 No H-bonds generated for 'chain 'e' and resid 170 through 172' Processing helix chain 'e' and resid 177 through 192 removed outlier: 3.633A pdb=" N ALA e 183 " --> pdb=" O GLU e 179 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN e 188 " --> pdb=" O ILE e 184 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TRP e 190 " --> pdb=" O ARG e 186 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA e 191 " --> pdb=" O GLU e 187 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 74 Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 241 removed outlier: 3.512A pdb=" N LEU A 270 " --> pdb=" O TYR A 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 239 through 241 removed outlier: 3.512A pdb=" N LEU A 270 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP A 369 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.763A pdb=" N PHE B 2 " --> pdb=" O PHE B 533 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 527 through 528 removed outlier: 3.576A pdb=" N LEU C 527 " --> pdb=" O TYR C 534 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 119 through 123 Processing sheet with id=AA7, first strand: chain 'D' and resid 168 through 170 removed outlier: 5.751A pdb=" N ILE D 168 " --> pdb=" O ILE D 196 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU D 198 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE D 276 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER D 315 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL D 278 " --> pdb=" O SER D 315 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N MET D 317 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE D 312 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N SER D 340 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU D 314 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL D 342 " --> pdb=" O LEU D 314 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ARG D 316 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 10.430A pdb=" N TYR D 344 " --> pdb=" O ARG D 316 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN D 318 " --> pdb=" O TYR D 344 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ASP D 346 " --> pdb=" O ASN D 318 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N LYS D 366 " --> pdb=" O ARG D 341 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA D 343 " --> pdb=" O LYS D 366 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LYS D 368 " --> pdb=" O ALA D 343 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE D 345 " --> pdb=" O LYS D 368 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE D 367 " --> pdb=" O PHE D 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 168 through 170 removed outlier: 5.751A pdb=" N ILE D 168 " --> pdb=" O ILE D 196 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU D 198 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE D 276 " --> pdb=" O ARG D 313 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER D 315 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL D 278 " --> pdb=" O SER D 315 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N MET D 317 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE D 312 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N SER D 340 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU D 314 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL D 342 " --> pdb=" O LEU D 314 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ARG D 316 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 10.430A pdb=" N TYR D 344 " --> pdb=" O ARG D 316 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN D 318 " --> pdb=" O TYR D 344 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ASP D 346 " --> pdb=" O ASN D 318 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL D 364 " --> pdb=" O ARG D 341 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA D 343 " --> pdb=" O VAL D 364 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE D 440 " --> pdb=" O GLU D 465 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N TYR D 467 " --> pdb=" O ILE D 440 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU D 442 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 326 through 327 removed outlier: 6.597A pdb=" N ALA D 326 " --> pdb=" O VAL D 351 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 392 through 394 removed outlier: 4.019A pdb=" N LEU D 413 " --> pdb=" O VAL D 477 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 15 through 19 removed outlier: 3.584A pdb=" N MET E 77 " --> pdb=" O VAL E 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 239 through 240 Processing sheet with id=AB4, first strand: chain 'b' and resid 527 through 528 Processing sheet with id=AB5, first strand: chain 'c' and resid 527 through 528 Processing sheet with id=AB6, first strand: chain 'd' and resid 119 through 123 removed outlier: 3.590A pdb=" N VAL d 140 " --> pdb=" O TYR d 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'd' and resid 168 through 171 removed outlier: 6.670A pdb=" N ILE d 168 " --> pdb=" O GLU d 198 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N GLN d 200 " --> pdb=" O ILE d 168 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE d 170 " --> pdb=" O GLN d 200 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY d 197 " --> pdb=" O LYS d 275 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N THR d 277 " --> pdb=" O GLY d 197 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL d 199 " --> pdb=" O THR d 277 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ARG d 279 " --> pdb=" O VAL d 199 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE d 201 " --> pdb=" O ARG d 279 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE d 276 " --> pdb=" O ARG d 313 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N SER d 315 " --> pdb=" O ILE d 276 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL d 278 " --> pdb=" O SER d 315 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE d 312 " --> pdb=" O VAL d 338 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N SER d 340 " --> pdb=" O ILE d 312 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU d 314 " --> pdb=" O SER d 340 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU d 337 " --> pdb=" O THR d 360 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LYS d 362 " --> pdb=" O LEU d 337 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU d 339 " --> pdb=" O LYS d 362 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE d 440 " --> pdb=" O GLU d 465 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TYR d 467 " --> pdb=" O ILE d 440 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU d 442 " --> pdb=" O TYR d 467 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 344 through 346 removed outlier: 6.756A pdb=" N ILE d 345 " --> pdb=" O LYS d 368 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE d 367 " --> pdb=" O PHE d 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'd' and resid 392 through 394 removed outlier: 3.765A pdb=" N VAL d 475 " --> pdb=" O ARG d 409 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU d 413 " --> pdb=" O VAL d 477 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL d 454 " --> pdb=" O ILE d 478 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'e' and resid 5 through 9 removed outlier: 3.903A pdb=" N PHE e 16 " --> pdb=" O LEU e 8 " (cutoff:3.500A) 1950 hydrogen bonds defined for protein. 5676 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 7.88 Time building geometry restraints manager: 5.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9919 1.33 - 1.45: 8835 1.45 - 1.58: 22089 1.58 - 1.70: 174 1.70 - 1.82: 262 Bond restraints: 41279 Sorted by residual: bond pdb=" C3' DT G 14 " pdb=" C2' DT G 14 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C1' DC G 2 " pdb=" N1 DC G 2 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 9.13e+00 bond pdb=" C3' DA F 4 " pdb=" C2' DA F 4 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.47e+00 bond pdb=" C3' DA F 11 " pdb=" C2' DA F 11 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.35e+00 bond pdb=" C3' DA G 29 " pdb=" C2' DA G 29 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.32e+00 ... (remaining 41274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 55486 2.27 - 4.55: 638 4.55 - 6.82: 70 6.82 - 9.09: 14 9.09 - 11.36: 3 Bond angle restraints: 56211 Sorted by residual: angle pdb=" N3 DT F 10 " pdb=" C4 DT F 10 " pdb=" O4 DT F 10 " ideal model delta sigma weight residual 119.90 122.98 -3.08 6.00e-01 2.78e+00 2.64e+01 angle pdb=" C ARG D 435 " pdb=" CA ARG D 435 " pdb=" CB ARG D 435 " ideal model delta sigma weight residual 117.23 110.30 6.93 1.36e+00 5.41e-01 2.60e+01 angle pdb=" O4 DT F 10 " pdb=" C4 DT F 10 " pdb=" C5 DT F 10 " ideal model delta sigma weight residual 124.90 121.57 3.33 7.00e-01 2.04e+00 2.26e+01 angle pdb=" N3 DT F 32 " pdb=" C4 DT F 32 " pdb=" O4 DT F 32 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT F 19 " pdb=" C4 DT F 19 " pdb=" O4 DT F 19 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.94e+01 ... (remaining 56206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.79: 23084 33.79 - 67.59: 1535 67.59 - 101.38: 73 101.38 - 135.18: 1 135.18 - 168.97: 3 Dihedral angle restraints: 24696 sinusoidal: 10916 harmonic: 13780 Sorted by residual: dihedral pdb=" CB CYS B 17 " pdb=" SG CYS B 17 " pdb=" SG CYS B 42 " pdb=" CB CYS B 42 " ideal model delta sinusoidal sigma weight residual -86.00 -6.60 -79.40 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CA SER d 42 " pdb=" C SER d 42 " pdb=" N ASN d 43 " pdb=" CA ASN d 43 " ideal model delta harmonic sigma weight residual 180.00 149.74 30.26 0 5.00e+00 4.00e-02 3.66e+01 dihedral pdb=" CA LEU a 224 " pdb=" C LEU a 224 " pdb=" N ASN a 225 " pdb=" CA ASN a 225 " ideal model delta harmonic sigma weight residual -180.00 -150.24 -29.76 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 24693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 5872 0.084 - 0.168: 313 0.168 - 0.251: 3 0.251 - 0.335: 0 0.335 - 0.419: 1 Chirality restraints: 6189 Sorted by residual: chirality pdb=" P DA G 1 " pdb=" OP1 DA G 1 " pdb=" OP2 DA G 1 " pdb=" O5' DA G 1 " both_signs ideal model delta sigma weight residual True 2.34 2.75 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" C3' DT F 18 " pdb=" C4' DT F 18 " pdb=" O3' DT F 18 " pdb=" C2' DT F 18 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" C3' DA G 29 " pdb=" C4' DA G 29 " pdb=" O3' DA G 29 " pdb=" C2' DA G 29 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 6186 not shown) Planarity restraints: 6798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 28 " -0.082 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO B 29 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO B 29 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 29 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 103 " 0.018 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C MET C 103 " -0.060 2.00e-02 2.50e+03 pdb=" O MET C 103 " 0.022 2.00e-02 2.50e+03 pdb=" N ASN C 104 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 163 " 0.015 2.00e-02 2.50e+03 3.14e-02 9.86e+00 pdb=" CG ASP A 163 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASP A 163 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP A 163 " 0.020 2.00e-02 2.50e+03 ... (remaining 6795 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 860 2.66 - 3.22: 40170 3.22 - 3.78: 67876 3.78 - 4.34: 87190 4.34 - 4.90: 139229 Nonbonded interactions: 335325 Sorted by model distance: nonbonded pdb=" OG1 THR A 503 " pdb=" OG SER A 506 " model vdw 2.097 3.040 nonbonded pdb=" OG SER E 162 " pdb=" OE1 GLU E 165 " model vdw 2.143 3.040 nonbonded pdb=" OD1 ASN D 419 " pdb=" OG1 THR D 422 " model vdw 2.149 3.040 nonbonded pdb=" OH TYR A 52 " pdb=" O PRO A 79 " model vdw 2.159 3.040 nonbonded pdb=" O GLU E 165 " pdb=" OG1 THR E 169 " model vdw 2.164 3.040 ... (remaining 335320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 97 or (resid 113 and (name N or name CA or name \ C or name O or name CB )) or resid 114 through 540)) selection = (chain 'a' and (resid 27 through 64 or resid 71 through 417 or resid 422 through \ 540)) } ncs_group { reference = (chain 'B' and (resid 6 through 23 or resid 53 through 313 or resid 340 through \ 562 or resid 564 or resid 589 through 608)) selection = (chain 'C' and (resid 6 through 23 or resid 53 through 313 or resid 340 through \ 562 or resid 564 or resid 589 through 608)) selection = (chain 'b' and (resid 6 through 313 or resid 340 through 608)) selection = (chain 'c' and (resid 6 through 23 or resid 53 through 562 or resid 564 or resid \ 589 through 608)) } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = (chain 'H' and resid 581 through 631) selection = (chain 'I' and resid 581 through 631) selection = (chain 'J' and resid 581 through 631) } 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: 5.300 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: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 44.350 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 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 : 0.004 0.074 41285 Z= 0.222 Angle : 0.600 12.131 56221 Z= 0.370 Chirality : 0.041 0.419 6189 Planarity : 0.004 0.123 6798 Dihedral : 19.941 168.971 15710 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.74 % Favored : 94.15 % Rotamer: Outliers : 4.32 % Allowed : 29.45 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.50 (0.13), residues: 4548 helix: 1.23 (0.10), residues: 2675 sheet: 0.02 (0.44), residues: 171 loop : -1.05 (0.16), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 265 TYR 0.024 0.001 TYR a 49 PHE 0.041 0.001 PHE H 593 TRP 0.044 0.002 TRP e 119 HIS 0.006 0.001 HIS I 619 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.22 (41279) covalent geometry : angle 0.59713 / 0.37 (56211) SS BOND : bond 0.00351 / 0.17 ( 2) SS BOND : angle 1.55813 / 0.82 ( 4) hydrogen bonds : bond 0.14388 / 9.75 ( 2000) hydrogen bonds : angle 5.50368 / 3.92 ( 5794) metal coordination : bond 0.01009 / 0.52 ( 4) metal coordination : angle 5.91879 / 2.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 403 time to evaluate : 1.665 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: A 124 LYS cc_start: 0.8893 (mttm) cc_final: 0.8678 (mtpt) REVERT: A 270 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.8003 (pp) REVERT: B 18 THR cc_start: 0.6143 (OUTLIER) cc_final: 0.5809 (m) REVERT: B 27 MET cc_start: 0.6103 (pmm) cc_final: 0.5697 (pmm) REVERT: B 43 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6040 (pmm) REVERT: B 103 MET cc_start: 0.8286 (mtp) cc_final: 0.8047 (mtp) REVERT: B 169 MET cc_start: 0.8638 (tmm) cc_final: 0.8235 (tmm) REVERT: B 232 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.6970 (mpp80) REVERT: B 345 TYR cc_start: 0.8335 (t80) cc_final: 0.8028 (t80) REVERT: B 418 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: B 420 ILE cc_start: 0.8360 (tt) cc_final: 0.8153 (tt) REVERT: B 446 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6418 (m-80) REVERT: B 473 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.8382 (t80) REVERT: C 43 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7685 (pmm) REVERT: C 169 MET cc_start: 0.8541 (ttt) cc_final: 0.8256 (ttp) REVERT: C 327 GLN cc_start: 0.8731 (pp30) cc_final: 0.8523 (pp30) REVERT: D 63 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8929 (tt) REVERT: D 193 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8298 (m-10) REVERT: D 284 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.8149 (t80) REVERT: D 320 ILE cc_start: 0.8847 (tt) cc_final: 0.8627 (tt) REVERT: D 327 ASP cc_start: 0.6136 (t0) cc_final: 0.5753 (p0) REVERT: E 1 MET cc_start: 0.2985 (mtp) cc_final: 0.2773 (tpt) REVERT: E 172 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7638 (pt) REVERT: H 575 GLU cc_start: 0.8391 (tp30) cc_final: 0.6867 (pm20) REVERT: I 597 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6494 (tp) REVERT: I 621 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8824 (tp) REVERT: I 629 ASP cc_start: 0.9132 (m-30) cc_final: 0.8878 (m-30) REVERT: J 614 ARG cc_start: 0.8288 (ttt180) cc_final: 0.7857 (ttm-80) REVERT: a 481 ASN cc_start: 0.8131 (t0) cc_final: 0.7802 (t0) REVERT: b 102 TRP cc_start: 0.6786 (m100) cc_final: 0.6378 (m100) REVERT: b 608 SER cc_start: 0.4256 (m) cc_final: 0.4002 (p) REVERT: c 92 LEU cc_start: 0.0932 (OUTLIER) cc_final: 0.0282 (pt) REVERT: d 1 MET cc_start: 0.3345 (ttt) cc_final: 0.2598 (tpp) outliers start: 187 outliers final: 61 residues processed: 567 average time/residue: 0.2563 time to fit residues: 238.1948 Evaluate side-chains 290 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 214 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 49 TYR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 325 TYR Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 228 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 284 TYR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 358 SER Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 449 PHE Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain I residue 597 LEU Chi-restraints excluded: chain I residue 621 LEU Chi-restraints excluded: chain I residue 635 SER Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain a residue 71 ASN Chi-restraints excluded: chain a residue 129 LEU Chi-restraints excluded: chain a residue 215 LEU Chi-restraints excluded: chain a residue 225 ASN Chi-restraints excluded: chain a residue 241 LEU Chi-restraints excluded: chain a residue 337 THR Chi-restraints excluded: chain a residue 497 SER Chi-restraints excluded: chain b residue 233 LEU Chi-restraints excluded: chain b residue 276 LEU Chi-restraints excluded: chain b residue 316 VAL Chi-restraints excluded: chain b residue 360 ASN Chi-restraints excluded: chain b residue 591 ARG Chi-restraints excluded: chain b residue 605 ASP Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 158 TYR Chi-restraints excluded: chain c residue 418 TYR Chi-restraints excluded: chain c residue 545 ILE Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain d residue 352 PHE Chi-restraints excluded: chain d residue 357 LYS Chi-restraints excluded: chain d residue 466 ILE Chi-restraints excluded: chain e residue 116 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 0.0980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 GLN D 164 ASN E 101 ASN E 188 ASN a 171 ASN ** a 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 116 ASN ** b 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 195 ASN ** c 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 262 HIS ** c 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 313 HIS ** c 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 355 ASN e 142 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.091896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.066187 restraints weight = 221248.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.066363 restraints weight = 117914.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.066747 restraints weight = 75702.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.067061 restraints weight = 57968.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.067663 restraints weight = 49765.515| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 41285 Z= 0.235 Angle : 0.706 14.220 56221 Z= 0.369 Chirality : 0.045 0.329 6189 Planarity : 0.005 0.121 6798 Dihedral : 15.480 171.467 6195 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.65 % Favored : 94.22 % Rotamer: Outliers : 5.48 % Allowed : 27.95 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.26 (0.13), residues: 4548 helix: 1.02 (0.10), residues: 2711 sheet: -0.24 (0.40), residues: 188 loop : -1.17 (0.16), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 20 TYR 0.043 0.002 TYR a 49 PHE 0.036 0.002 PHE H 593 TRP 0.039 0.002 TRP c 200 HIS 0.010 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.24 (41279) covalent geometry : angle 0.70124 / 0.37 (56211) SS BOND : bond 0.00602 / 0.29 ( 2) SS BOND : angle 1.17322 / 0.59 ( 4) hydrogen bonds : bond 0.04933 / 3.31 ( 2000) hydrogen bonds : angle 4.86436 / 3.46 ( 5794) metal coordination : bond 0.01601 / 0.81 ( 4) metal coordination : angle 7.92050 / 3.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 231 time to evaluate : 1.714 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: A 166 LYS cc_start: 0.8817 (tppt) cc_final: 0.8589 (tppt) REVERT: A 270 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7810 (pp) REVERT: A 323 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8308 (mm) REVERT: A 386 TRP cc_start: 0.8333 (OUTLIER) cc_final: 0.5759 (p-90) REVERT: A 504 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8017 (mm) REVERT: B 43 MET cc_start: 0.6903 (pmm) cc_final: 0.6670 (pmm) REVERT: B 169 MET cc_start: 0.8568 (tmm) cc_final: 0.8111 (tmm) REVERT: B 232 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7288 (mpp80) REVERT: B 418 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: B 446 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6526 (m-80) REVERT: B 460 MET cc_start: 0.8102 (tmm) cc_final: 0.7710 (tmm) REVERT: B 473 TYR cc_start: 0.8945 (OUTLIER) cc_final: 0.8589 (t80) REVERT: B 598 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8578 (mm-40) REVERT: C 103 MET cc_start: 0.8668 (mtm) cc_final: 0.8428 (mtt) REVERT: C 169 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8270 (ttp) REVERT: C 171 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7722 (mm) REVERT: C 418 TYR cc_start: 0.9218 (OUTLIER) cc_final: 0.7806 (m-80) REVERT: D 193 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8334 (m-10) REVERT: D 287 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9082 (mt) REVERT: D 294 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6578 (ptt-90) REVERT: D 449 PHE cc_start: 0.6717 (OUTLIER) cc_final: 0.6495 (m-10) REVERT: E 1 MET cc_start: 0.2808 (mtp) cc_final: 0.2393 (tpt) REVERT: E 172 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7834 (pt) REVERT: H 575 GLU cc_start: 0.8718 (tp30) cc_final: 0.6580 (pm20) REVERT: I 597 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6533 (tp) REVERT: J 614 ARG cc_start: 0.8220 (ttt180) cc_final: 0.7882 (ttm-80) REVERT: a 407 MET cc_start: 0.8370 (mmm) cc_final: 0.8085 (mmm) REVERT: a 481 ASN cc_start: 0.8459 (t0) cc_final: 0.8109 (t0) REVERT: b 1 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6683 (ptt) REVERT: b 446 PHE cc_start: 0.3934 (OUTLIER) cc_final: 0.3624 (m-80) REVERT: c 43 MET cc_start: -0.0921 (tpt) cc_final: -0.2268 (mmp) REVERT: c 479 SER cc_start: 0.3924 (OUTLIER) cc_final: 0.3656 (m) REVERT: d 1 MET cc_start: 0.5571 (ttt) cc_final: 0.4387 (tpp) REVERT: d 92 PHE cc_start: 0.7421 (OUTLIER) cc_final: 0.7207 (p90) REVERT: d 189 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8061 (pp30) REVERT: e 1 MET cc_start: 0.3653 (tmm) cc_final: 0.3291 (tmm) REVERT: e 85 SER cc_start: 0.8041 (OUTLIER) cc_final: 0.7719 (p) REVERT: e 89 LYS cc_start: 0.9078 (mmmt) cc_final: 0.8770 (mtpp) REVERT: e 130 MET cc_start: 0.9092 (tmt) cc_final: 0.8702 (mmm) outliers start: 237 outliers final: 100 residues processed: 451 average time/residue: 0.2428 time to fit residues: 181.4945 Evaluate side-chains 318 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 194 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 TYR Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 182 CYS Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 487 VAL Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 335 TYR Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 29 CYS Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 449 PHE Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain H residue 606 LYS Chi-restraints excluded: chain H residue 628 LEU Chi-restraints excluded: chain I residue 597 LEU Chi-restraints excluded: chain I residue 599 VAL Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 599 VAL Chi-restraints excluded: chain a residue 49 TYR Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 128 SER Chi-restraints excluded: chain a residue 129 LEU Chi-restraints excluded: chain a residue 207 THR Chi-restraints excluded: chain a residue 215 LEU Chi-restraints excluded: chain a residue 217 ASP Chi-restraints excluded: chain a residue 241 LEU Chi-restraints excluded: chain a residue 297 ILE Chi-restraints excluded: chain a residue 337 THR Chi-restraints excluded: chain a residue 338 PHE Chi-restraints excluded: chain a residue 344 THR Chi-restraints excluded: chain a residue 484 ILE Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 111 SER Chi-restraints excluded: chain b residue 121 ASN Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 149 ASP Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain b residue 233 LEU Chi-restraints excluded: chain b residue 276 LEU Chi-restraints excluded: chain b residue 316 VAL Chi-restraints excluded: chain b residue 336 ARG Chi-restraints excluded: chain b residue 360 ASN Chi-restraints excluded: chain b residue 446 PHE Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 418 TYR Chi-restraints excluded: chain c residue 479 SER Chi-restraints excluded: chain c residue 545 ILE Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 92 PHE Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain d residue 189 GLN Chi-restraints excluded: chain d residue 254 GLN Chi-restraints excluded: chain d residue 257 SER Chi-restraints excluded: chain d residue 352 PHE Chi-restraints excluded: chain d residue 361 MET Chi-restraints excluded: chain d residue 454 VAL Chi-restraints excluded: chain d residue 466 ILE Chi-restraints excluded: chain e residue 82 VAL Chi-restraints excluded: chain e residue 85 SER Chi-restraints excluded: chain e residue 116 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 113 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 434 optimal weight: 20.0000 chunk 165 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 458 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 GLN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** J 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 622 ASN ** a 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 262 HIS ** c 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 108 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.092311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.066065 restraints weight = 208674.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.065400 restraints weight = 117830.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.065509 restraints weight = 75325.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.065879 restraints weight = 56786.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.066205 restraints weight = 47679.108| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 41285 Z= 0.134 Angle : 0.620 11.197 56221 Z= 0.324 Chirality : 0.042 0.338 6189 Planarity : 0.004 0.118 6798 Dihedral : 15.313 172.655 6140 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.06 % Favored : 94.81 % Rotamer: Outliers : 3.93 % Allowed : 27.72 % Favored : 68.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.37 (0.13), residues: 4548 helix: 1.08 (0.10), residues: 2704 sheet: 0.00 (0.41), residues: 184 loop : -1.08 (0.16), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG c 392 TYR 0.042 0.001 TYR a 49 PHE 0.035 0.001 PHE H 593 TRP 0.049 0.002 TRP c 200 HIS 0.009 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (41279) covalent geometry : angle 0.61630 / 0.32 (56211) SS BOND : bond 0.00395 / 0.19 ( 2) SS BOND : angle 2.63393 / 1.35 ( 4) hydrogen bonds : bond 0.04421 / 2.95 ( 2000) hydrogen bonds : angle 4.58077 / 3.27 ( 5794) metal coordination : bond 0.01139 / 0.59 ( 4) metal coordination : angle 5.84604 / 2.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 222 time to evaluate : 1.585 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: A 89 LEU cc_start: 0.8474 (mt) cc_final: 0.8209 (mt) REVERT: A 166 LYS cc_start: 0.8906 (tppt) cc_final: 0.8674 (tppt) REVERT: A 270 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7629 (pp) REVERT: A 323 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8112 (mm) REVERT: A 386 TRP cc_start: 0.8106 (OUTLIER) cc_final: 0.5454 (p-90) REVERT: A 504 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8118 (mm) REVERT: B 43 MET cc_start: 0.6617 (pmm) cc_final: 0.5974 (pmm) REVERT: B 169 MET cc_start: 0.8579 (tmm) cc_final: 0.8176 (tmm) REVERT: B 232 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7298 (mpp80) REVERT: B 418 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.8201 (m-80) REVERT: B 446 PHE cc_start: 0.7005 (OUTLIER) cc_final: 0.6257 (m-80) REVERT: B 460 MET cc_start: 0.8030 (tmm) cc_final: 0.7553 (tmm) REVERT: B 598 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8465 (mm-40) REVERT: C 169 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8280 (ttp) REVERT: C 555 MET cc_start: 0.6748 (tmm) cc_final: 0.6521 (tmm) REVERT: D 193 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.8291 (m-10) REVERT: D 327 ASP cc_start: 0.6589 (t0) cc_final: 0.6168 (m-30) REVERT: D 449 PHE cc_start: 0.6567 (OUTLIER) cc_final: 0.6367 (m-10) REVERT: E 1 MET cc_start: 0.2906 (mtp) cc_final: 0.2521 (tpt) REVERT: E 172 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7580 (pt) REVERT: H 616 TYR cc_start: 0.8290 (t80) cc_final: 0.7916 (t80) REVERT: I 597 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6520 (tp) REVERT: I 600 PHE cc_start: 0.8017 (t80) cc_final: 0.7732 (t80) REVERT: I 606 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8501 (tppt) REVERT: J 614 ARG cc_start: 0.8083 (ttt180) cc_final: 0.7670 (ttm-80) REVERT: a 191 ASN cc_start: 0.8504 (t0) cc_final: 0.7896 (m110) REVERT: a 398 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8819 (mtpt) REVERT: a 407 MET cc_start: 0.8332 (mmm) cc_final: 0.8024 (mmm) REVERT: a 481 ASN cc_start: 0.8435 (t0) cc_final: 0.8152 (t0) REVERT: a 533 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8717 (mm) REVERT: b 1 MET cc_start: 0.6901 (ptp) cc_final: 0.6521 (ptt) REVERT: b 103 MET cc_start: 0.3618 (ttp) cc_final: 0.3370 (tpp) REVERT: b 460 MET cc_start: 0.8443 (ppp) cc_final: 0.8160 (ppp) REVERT: c 43 MET cc_start: -0.0417 (tpt) cc_final: -0.1612 (mmp) REVERT: c 115 MET cc_start: -0.5173 (ttt) cc_final: -0.5447 (ttt) REVERT: d 1 MET cc_start: 0.5879 (ttt) cc_final: 0.4711 (tpp) REVERT: d 127 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8329 (tp) REVERT: d 189 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8110 (pp30) REVERT: e 1 MET cc_start: 0.4323 (tmm) cc_final: 0.4089 (tmm) outliers start: 170 outliers final: 73 residues processed: 374 average time/residue: 0.2462 time to fit residues: 154.5231 Evaluate side-chains 289 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 199 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 335 TYR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 449 PHE Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain H residue 580 GLN Chi-restraints excluded: chain H residue 628 LEU Chi-restraints excluded: chain I residue 597 LEU Chi-restraints excluded: chain I residue 599 VAL Chi-restraints excluded: chain I residue 604 PHE Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 599 VAL Chi-restraints excluded: chain J residue 621 LEU Chi-restraints excluded: chain a residue 49 TYR Chi-restraints excluded: chain a residue 129 LEU Chi-restraints excluded: chain a residue 215 LEU Chi-restraints excluded: chain a residue 241 LEU Chi-restraints excluded: chain a residue 338 PHE Chi-restraints excluded: chain a residue 398 LYS Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 121 ASN Chi-restraints excluded: chain b residue 149 ASP Chi-restraints excluded: chain b residue 154 VAL Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain b residue 276 LEU Chi-restraints excluded: chain b residue 316 VAL Chi-restraints excluded: chain b residue 320 LEU Chi-restraints excluded: chain b residue 360 ASN Chi-restraints excluded: chain c residue 32 ASN Chi-restraints excluded: chain c residue 459 VAL Chi-restraints excluded: chain c residue 545 ILE Chi-restraints excluded: chain d residue 16 ILE Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 127 LEU Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain d residue 189 GLN Chi-restraints excluded: chain d residue 254 GLN Chi-restraints excluded: chain d residue 257 SER Chi-restraints excluded: chain d residue 320 ILE Chi-restraints excluded: chain d residue 352 PHE Chi-restraints excluded: chain d residue 357 LYS Chi-restraints excluded: chain d residue 363 ARG Chi-restraints excluded: chain d residue 450 ASN Chi-restraints excluded: chain d residue 454 VAL Chi-restraints excluded: chain d residue 466 ILE Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain e residue 82 VAL Chi-restraints excluded: chain e residue 116 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 304 optimal weight: 7.9990 chunk 430 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 381 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 368 optimal weight: 30.0000 chunk 425 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 HIS C 321 GLN D 318 ASN D 450 ASN E 88 GLN E 101 ASN E 188 ASN ** J 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 339 ASN ** b 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.091074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.065676 restraints weight = 224592.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.065595 restraints weight = 120630.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.066069 restraints weight = 76737.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.066436 restraints weight = 57819.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.066704 restraints weight = 49430.531| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 41285 Z= 0.207 Angle : 0.646 11.285 56221 Z= 0.336 Chirality : 0.043 0.341 6189 Planarity : 0.004 0.119 6798 Dihedral : 15.334 174.875 6125 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.32 % Favored : 94.55 % Rotamer: Outliers : 4.44 % Allowed : 26.91 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.36 (0.13), residues: 4548 helix: 1.07 (0.10), residues: 2705 sheet: -0.12 (0.40), residues: 190 loop : -1.06 (0.16), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG a 244 TYR 0.034 0.002 TYR a 49 PHE 0.037 0.002 PHE H 593 TRP 0.039 0.002 TRP c 200 HIS 0.008 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 (41279) covalent geometry : angle 0.64247 / 0.34 (56211) SS BOND : bond 0.00493 / 0.24 ( 2) SS BOND : angle 2.27859 / 1.16 ( 4) hydrogen bonds : bond 0.04383 / 2.93 ( 2000) hydrogen bonds : angle 4.58956 / 3.28 ( 5794) metal coordination : bond 0.01620 / 0.83 ( 4) metal coordination : angle 6.47320 / 3.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 208 time to evaluate : 1.572 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: A 89 LEU cc_start: 0.8608 (mt) cc_final: 0.8335 (mt) REVERT: A 166 LYS cc_start: 0.8910 (tppt) cc_final: 0.8655 (tppt) REVERT: A 270 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7604 (pp) REVERT: A 323 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8564 (mm) REVERT: A 386 TRP cc_start: 0.8301 (OUTLIER) cc_final: 0.5710 (p-90) REVERT: A 504 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8178 (mm) REVERT: B 27 MET cc_start: 0.6176 (ptp) cc_final: 0.5833 (pmm) REVERT: B 169 MET cc_start: 0.8576 (tmm) cc_final: 0.8119 (tmm) REVERT: B 232 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7325 (mpp80) REVERT: B 418 TYR cc_start: 0.9118 (OUTLIER) cc_final: 0.8577 (m-10) REVERT: B 446 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6481 (m-80) REVERT: B 460 MET cc_start: 0.8161 (tmm) cc_final: 0.7921 (tmm) REVERT: B 473 TYR cc_start: 0.8962 (OUTLIER) cc_final: 0.8546 (t80) REVERT: B 598 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8575 (mm-40) REVERT: C 43 MET cc_start: 0.8002 (pmm) cc_final: 0.7754 (pmm) REVERT: C 169 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8286 (ttp) REVERT: C 555 MET cc_start: 0.6902 (tmm) cc_final: 0.6687 (tmm) REVERT: D 193 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8487 (m-10) REVERT: D 294 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6679 (ptt-90) REVERT: D 449 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.6375 (m-10) REVERT: E 1 MET cc_start: 0.2919 (mtp) cc_final: 0.2574 (tpt) REVERT: E 172 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7854 (pt) REVERT: E 189 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7947 (tp30) REVERT: H 584 TYR cc_start: 0.7817 (m-10) cc_final: 0.7494 (m-80) REVERT: I 597 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6667 (tp) REVERT: I 604 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8088 (t80) REVERT: J 614 ARG cc_start: 0.8168 (ttt180) cc_final: 0.7802 (ttm-80) REVERT: a 191 ASN cc_start: 0.8588 (t0) cc_final: 0.8008 (m-40) REVERT: a 398 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8819 (mtpt) REVERT: a 407 MET cc_start: 0.8490 (mmm) cc_final: 0.8156 (mmm) REVERT: a 450 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7327 (pp) REVERT: a 481 ASN cc_start: 0.8485 (t0) cc_final: 0.8188 (t0) REVERT: a 533 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8719 (mm) REVERT: b 1 MET cc_start: 0.6746 (ptp) cc_final: 0.6270 (ptt) REVERT: c 43 MET cc_start: -0.0469 (tpt) cc_final: -0.1699 (mmp) REVERT: d 1 MET cc_start: 0.5227 (ttt) cc_final: 0.4045 (tpp) REVERT: d 62 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8512 (mp) REVERT: d 189 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8047 (pp30) REVERT: d 363 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7802 (mtm-85) REVERT: e 1 MET cc_start: 0.3723 (tmm) cc_final: 0.3478 (tmm) outliers start: 192 outliers final: 106 residues processed: 385 average time/residue: 0.2327 time to fit residues: 151.1953 Evaluate side-chains 318 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 189 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 335 TYR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain D residue 449 PHE Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain H residue 628 LEU Chi-restraints excluded: chain I residue 597 LEU Chi-restraints excluded: chain I residue 599 VAL Chi-restraints excluded: chain I residue 604 PHE Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 599 VAL Chi-restraints excluded: chain J residue 621 LEU Chi-restraints excluded: chain a residue 49 TYR Chi-restraints excluded: chain a residue 71 ASN Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 128 SER Chi-restraints excluded: chain a residue 190 LEU Chi-restraints excluded: chain a residue 215 LEU Chi-restraints excluded: chain a residue 217 ASP Chi-restraints excluded: chain a residue 241 LEU Chi-restraints excluded: chain a residue 297 ILE Chi-restraints excluded: chain a residue 338 PHE Chi-restraints excluded: chain a residue 398 LYS Chi-restraints excluded: chain a residue 414 THR Chi-restraints excluded: chain a residue 450 LEU Chi-restraints excluded: chain a residue 484 ILE Chi-restraints excluded: chain a residue 489 ILE Chi-restraints excluded: chain a residue 528 THR Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 111 SER Chi-restraints excluded: chain b residue 121 ASN Chi-restraints excluded: chain b residue 149 ASP Chi-restraints excluded: chain b residue 154 VAL Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain b residue 233 LEU Chi-restraints excluded: chain b residue 276 LEU Chi-restraints excluded: chain b residue 316 VAL Chi-restraints excluded: chain b residue 320 LEU Chi-restraints excluded: chain b residue 336 ARG Chi-restraints excluded: chain b residue 360 ASN Chi-restraints excluded: chain c residue 32 ASN Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 545 ILE Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain d residue 165 VAL Chi-restraints excluded: chain d residue 189 GLN Chi-restraints excluded: chain d residue 254 GLN Chi-restraints excluded: chain d residue 257 SER Chi-restraints excluded: chain d residue 352 PHE Chi-restraints excluded: chain d residue 357 LYS Chi-restraints excluded: chain d residue 363 ARG Chi-restraints excluded: chain d residue 450 ASN Chi-restraints excluded: chain d residue 454 VAL Chi-restraints excluded: chain d residue 466 ILE Chi-restraints excluded: chain d residue 471 LYS Chi-restraints excluded: chain e residue 33 LEU Chi-restraints excluded: chain e residue 116 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 94 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 443 optimal weight: 30.0000 chunk 65 optimal weight: 1.9990 chunk 304 optimal weight: 20.0000 chunk 332 optimal weight: 9.9990 chunk 426 optimal weight: 2.9990 chunk 351 optimal weight: 0.7980 chunk 293 optimal weight: 0.9990 chunk 395 optimal weight: 2.9990 chunk 450 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** H 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 601 ASN ** J 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 443 GLN e 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.090945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.065609 restraints weight = 210466.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.065450 restraints weight = 123961.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.065821 restraints weight = 77268.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.066251 restraints weight = 53296.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.066141 restraints weight = 51440.589| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 41285 Z= 0.143 Angle : 0.609 15.758 56221 Z= 0.316 Chirality : 0.042 0.347 6189 Planarity : 0.004 0.117 6798 Dihedral : 15.301 175.842 6122 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.12 % Favored : 94.74 % Rotamer: Outliers : 3.72 % Allowed : 27.25 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.45 (0.13), residues: 4548 helix: 1.13 (0.10), residues: 2705 sheet: -0.02 (0.41), residues: 184 loop : -1.00 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 244 TYR 0.036 0.001 TYR a 49 PHE 0.041 0.001 PHE H 593 TRP 0.028 0.001 TRP c 200 HIS 0.012 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (41279) covalent geometry : angle 0.60588 / 0.32 (56211) SS BOND : bond 0.00441 / 0.21 ( 2) SS BOND : angle 2.03659 / 1.02 ( 4) hydrogen bonds : bond 0.04114 / 2.73 ( 2000) hydrogen bonds : angle 4.47007 / 3.19 ( 5794) metal coordination : bond 0.01201 / 0.62 ( 4) metal coordination : angle 5.97159 / 2.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 201 time to evaluate : 1.143 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: A 89 LEU cc_start: 0.8697 (mt) cc_final: 0.8366 (mt) REVERT: A 166 LYS cc_start: 0.8873 (tppt) cc_final: 0.8587 (tppt) REVERT: A 270 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7572 (pp) REVERT: A 323 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8530 (mm) REVERT: A 386 TRP cc_start: 0.8194 (OUTLIER) cc_final: 0.5527 (p-90) REVERT: A 504 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8036 (mm) REVERT: B 27 MET cc_start: 0.6052 (ptp) cc_final: 0.5803 (pmm) REVERT: B 43 MET cc_start: 0.6615 (pmm) cc_final: 0.5635 (pmm) REVERT: B 115 MET cc_start: 0.8196 (mtp) cc_final: 0.7672 (ttp) REVERT: B 169 MET cc_start: 0.8593 (tmm) cc_final: 0.8200 (tmm) REVERT: B 232 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7264 (mpp80) REVERT: B 446 PHE cc_start: 0.7163 (OUTLIER) cc_final: 0.6513 (m-80) REVERT: B 460 MET cc_start: 0.8179 (tmm) cc_final: 0.7922 (tmm) REVERT: B 598 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8477 (mm-40) REVERT: C 43 MET cc_start: 0.7931 (pmm) cc_final: 0.7653 (pmm) REVERT: C 169 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8268 (ttp) REVERT: C 555 MET cc_start: 0.6801 (tmm) cc_final: 0.6521 (tmm) REVERT: D 193 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.8386 (m-10) REVERT: D 294 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6527 (ptt-90) REVERT: E 1 MET cc_start: 0.2908 (mtp) cc_final: 0.2677 (tpt) REVERT: E 130 MET cc_start: 0.8452 (tmm) cc_final: 0.8219 (tmm) REVERT: E 172 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7710 (pt) REVERT: I 597 LEU cc_start: 0.6677 (OUTLIER) cc_final: 0.6261 (tp) REVERT: I 601 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7823 (m-40) REVERT: I 604 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8209 (t80) REVERT: J 614 ARG cc_start: 0.7800 (ttt180) cc_final: 0.7479 (ttm-80) REVERT: a 191 ASN cc_start: 0.8550 (t0) cc_final: 0.7940 (m-40) REVERT: a 398 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8815 (mtpt) REVERT: a 407 MET cc_start: 0.8409 (mmm) cc_final: 0.8201 (mmt) REVERT: a 481 ASN cc_start: 0.8467 (t0) cc_final: 0.8181 (t0) REVERT: a 533 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8733 (mm) REVERT: b 1 MET cc_start: 0.6573 (ptp) cc_final: 0.6025 (ptt) REVERT: b 555 MET cc_start: 0.6125 (mmm) cc_final: 0.4615 (ppp) REVERT: c 43 MET cc_start: -0.0708 (tpt) cc_final: -0.2051 (mmp) REVERT: c 239 ILE cc_start: 0.5667 (OUTLIER) cc_final: 0.5428 (mt) REVERT: d 1 MET cc_start: 0.5344 (ttt) cc_final: 0.4254 (tpp) REVERT: d 65 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8444 (m-80) REVERT: d 189 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.8075 (pp30) REVERT: e 1 MET cc_start: 0.3676 (tmm) cc_final: 0.3441 (tmm) outliers start: 161 outliers final: 101 residues processed: 348 average time/residue: 0.2148 time to fit residues: 127.8260 Evaluate side-chains 308 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 188 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 223 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 335 TYR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 96 TYR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain H residue 628 LEU Chi-restraints excluded: chain I residue 597 LEU Chi-restraints excluded: chain I residue 599 VAL Chi-restraints excluded: chain I residue 601 ASN Chi-restraints excluded: chain I residue 604 PHE Chi-restraints excluded: chain I residue 618 LEU Chi-restraints excluded: chain J residue 590 LEU Chi-restraints excluded: chain J residue 599 VAL Chi-restraints excluded: chain a residue 49 TYR Chi-restraints excluded: chain a residue 71 ASN Chi-restraints excluded: chain a residue 128 SER Chi-restraints excluded: chain a residue 190 LEU Chi-restraints excluded: chain a residue 215 LEU Chi-restraints excluded: chain a residue 217 ASP Chi-restraints excluded: chain a residue 241 LEU Chi-restraints excluded: chain a residue 297 ILE Chi-restraints excluded: chain a residue 338 PHE Chi-restraints excluded: chain a residue 379 ASN Chi-restraints excluded: chain a residue 398 LYS Chi-restraints excluded: chain a residue 528 THR Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 121 ASN Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 149 ASP Chi-restraints excluded: chain b residue 154 VAL Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain b residue 233 LEU Chi-restraints excluded: chain b residue 276 LEU Chi-restraints excluded: chain b residue 316 VAL Chi-restraints excluded: chain b residue 320 LEU Chi-restraints excluded: chain b residue 360 ASN Chi-restraints excluded: chain b residue 554 GLU Chi-restraints excluded: chain c residue 32 ASN Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 239 ILE Chi-restraints excluded: chain c residue 459 VAL Chi-restraints excluded: chain c residue 477 VAL Chi-restraints excluded: chain c residue 545 ILE Chi-restraints excluded: chain d residue 65 TYR Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain d residue 165 VAL Chi-restraints excluded: chain d residue 189 GLN Chi-restraints excluded: chain d residue 254 GLN Chi-restraints excluded: chain d residue 257 SER Chi-restraints excluded: chain d residue 357 LYS Chi-restraints excluded: chain d residue 361 MET Chi-restraints excluded: chain d residue 363 ARG Chi-restraints excluded: chain d residue 443 GLN Chi-restraints excluded: chain d residue 450 ASN Chi-restraints excluded: chain d residue 454 VAL Chi-restraints excluded: chain d residue 466 ILE Chi-restraints excluded: chain d residue 471 LYS Chi-restraints excluded: chain e residue 116 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 270 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 288 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 290 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 201 optimal weight: 0.3980 chunk 222 optimal weight: 20.0000 chunk 250 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN E 188 ASN H 580 GLN ** H 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 327 GLN b 394 ASN ** b 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 108 HIS d 407 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.091289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.065309 restraints weight = 209941.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.064334 restraints weight = 118560.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.064446 restraints weight = 76416.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.064762 restraints weight = 56938.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.065072 restraints weight = 48648.685| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 41285 Z= 0.122 Angle : 0.596 11.970 56221 Z= 0.309 Chirality : 0.041 0.345 6189 Planarity : 0.004 0.116 6798 Dihedral : 15.257 177.011 6114 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.08 % Favored : 94.79 % Rotamer: Outliers : 3.33 % Allowed : 27.37 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.46 (0.13), residues: 4548 helix: 1.13 (0.10), residues: 2713 sheet: -0.02 (0.41), residues: 189 loop : -1.00 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 244 TYR 0.039 0.001 TYR H 584 PHE 0.042 0.001 PHE H 593 TRP 0.029 0.001 TRP c 200 HIS 0.011 0.001 HIS c 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (41279) covalent geometry : angle 0.59286 / 0.31 (56211) SS BOND : bond 0.00314 / 0.15 ( 2) SS BOND : angle 1.87113 / 0.94 ( 4) hydrogen bonds : bond 0.03982 / 2.63 ( 2000) hydrogen bonds : angle 4.39957 / 3.14 ( 5794) metal coordination : bond 0.01050 / 0.55 ( 4) metal coordination : angle 5.38625 / 2.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 200 time to evaluate : 0.945 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: A 89 LEU cc_start: 0.8646 (mt) cc_final: 0.8292 (mt) REVERT: A 166 LYS cc_start: 0.8866 (tppt) cc_final: 0.8577 (tppt) REVERT: A 234 ILE cc_start: 0.9217 (tt) cc_final: 0.8949 (mt) REVERT: A 270 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7564 (pp) REVERT: A 323 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8427 (mm) REVERT: A 386 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.5674 (p-90) REVERT: A 504 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7970 (mm) REVERT: B 43 MET cc_start: 0.6497 (pmm) cc_final: 0.5578 (pmm) REVERT: B 169 MET cc_start: 0.8544 (tmm) cc_final: 0.8160 (tmm) REVERT: B 232 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7372 (mpp80) REVERT: B 418 TYR cc_start: 0.9047 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: B 446 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: B 460 MET cc_start: 0.8101 (tmm) cc_final: 0.7874 (tmm) REVERT: C 43 MET cc_start: 0.7906 (pmm) cc_final: 0.7650 (pmm) REVERT: C 169 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8243 (ttp) REVERT: C 555 MET cc_start: 0.6765 (tmm) cc_final: 0.6558 (tmm) REVERT: D 193 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8390 (m-10) REVERT: D 287 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9027 (mt) REVERT: D 327 ASP cc_start: 0.6487 (OUTLIER) cc_final: 0.6097 (m-30) REVERT: E 1 MET cc_start: 0.2930 (mtp) cc_final: 0.2704 (tpt) REVERT: E 130 MET cc_start: 0.8449 (tmm) cc_final: 0.8191 (tmm) REVERT: E 172 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7549 (pt) REVERT: I 597 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6772 (tp) REVERT: I 604 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8307 (t80) REVERT: J 593 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8248 (m-80) REVERT: J 614 ARG cc_start: 0.8045 (ttt180) cc_final: 0.7587 (ttm-80) REVERT: a 191 ASN cc_start: 0.8504 (t0) cc_final: 0.7912 (m-40) REVERT: a 398 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8860 (mtpt) REVERT: a 407 MET cc_start: 0.8302 (mmm) cc_final: 0.8100 (mmt) REVERT: a 481 ASN cc_start: 0.8369 (t0) cc_final: 0.8084 (t0) REVERT: a 533 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8706 (mm) REVERT: b 1 MET cc_start: 0.6972 (ptp) cc_final: 0.6620 (ptt) REVERT: b 328 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6594 (p0) REVERT: b 377 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9043 (mt) REVERT: b 555 MET cc_start: 0.6197 (mmm) cc_final: 0.5186 (ppp) REVERT: c 43 MET cc_start: -0.0413 (tpt) cc_final: -0.1571 (mmp) REVERT: d 1 MET cc_start: 0.5541 (ttt) cc_final: 0.4093 (tpp) REVERT: d 65 TYR cc_start: 0.8778 (OUTLIER) cc_final: 0.8310 (m-80) REVERT: d 173 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7257 (m-30) REVERT: d 189 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8018 (pp30) REVERT: e 1 MET cc_start: 0.4207 (tmm) cc_final: 0.3975 (tmm) outliers start: 144 outliers final: 82 residues processed: 333 average time/residue: 0.2113 time to fit residues: 120.1561 Evaluate side-chains 295 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 191 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 335 TYR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain H residue 628 LEU Chi-restraints excluded: chain I residue 597 LEU Chi-restraints excluded: chain I residue 599 VAL Chi-restraints excluded: chain I residue 604 PHE Chi-restraints excluded: chain J residue 593 PHE Chi-restraints excluded: chain J residue 599 VAL Chi-restraints excluded: chain a residue 49 TYR Chi-restraints excluded: chain a residue 71 ASN Chi-restraints excluded: chain a residue 75 TYR Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 128 SER Chi-restraints excluded: chain a residue 190 LEU Chi-restraints excluded: chain a residue 215 LEU Chi-restraints excluded: chain a residue 241 LEU Chi-restraints excluded: chain a residue 338 PHE Chi-restraints excluded: chain a residue 379 ASN Chi-restraints excluded: chain a residue 398 LYS Chi-restraints excluded: chain a residue 528 THR Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 121 ASN Chi-restraints excluded: chain b residue 149 ASP Chi-restraints excluded: chain b residue 154 VAL Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain b residue 233 LEU Chi-restraints excluded: chain b residue 276 LEU Chi-restraints excluded: chain b residue 316 VAL Chi-restraints excluded: chain b residue 320 LEU Chi-restraints excluded: chain b residue 328 ASP Chi-restraints excluded: chain b residue 360 ASN Chi-restraints excluded: chain b residue 377 LEU Chi-restraints excluded: chain b residue 554 GLU Chi-restraints excluded: chain b residue 600 GLU Chi-restraints excluded: chain c residue 32 ASN Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 459 VAL Chi-restraints excluded: chain c residue 477 VAL Chi-restraints excluded: chain c residue 545 ILE Chi-restraints excluded: chain d residue 65 TYR Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain d residue 173 ASP Chi-restraints excluded: chain d residue 189 GLN Chi-restraints excluded: chain d residue 254 GLN Chi-restraints excluded: chain d residue 361 MET Chi-restraints excluded: chain d residue 363 ARG Chi-restraints excluded: chain d residue 454 VAL Chi-restraints excluded: chain d residue 466 ILE Chi-restraints excluded: chain d residue 471 LYS Chi-restraints excluded: chain d residue 478 ILE Chi-restraints excluded: chain e residue 116 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 51 optimal weight: 9.9990 chunk 274 optimal weight: 4.9990 chunk 138 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 163 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 214 optimal weight: 6.9990 chunk 151 optimal weight: 0.7980 chunk 353 optimal weight: 5.9990 chunk 272 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 ASN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN H 579 GLN ** J 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 327 GLN ** b 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 5 ASN d 164 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.090888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.065239 restraints weight = 211633.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.065857 restraints weight = 122941.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.065755 restraints weight = 73406.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.065588 restraints weight = 51785.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.065710 restraints weight = 50591.344| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 41285 Z= 0.145 Angle : 0.613 15.443 56221 Z= 0.316 Chirality : 0.041 0.348 6189 Planarity : 0.004 0.114 6798 Dihedral : 15.263 177.758 6112 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.06 % Favored : 94.81 % Rotamer: Outliers : 3.37 % Allowed : 27.30 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.47 (0.13), residues: 4548 helix: 1.13 (0.10), residues: 2712 sheet: -0.05 (0.41), residues: 184 loop : -0.97 (0.16), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 262 TYR 0.037 0.001 TYR a 49 PHE 0.050 0.001 PHE I 600 TRP 0.032 0.001 TRP c 200 HIS 0.013 0.001 HIS c 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (41279) covalent geometry : angle 0.61015 / 0.32 (56211) SS BOND : bond 0.00327 / 0.16 ( 2) SS BOND : angle 1.87660 / 0.94 ( 4) hydrogen bonds : bond 0.03978 / 2.62 ( 2000) hydrogen bonds : angle 4.40137 / 3.16 ( 5794) metal coordination : bond 0.01203 / 0.62 ( 4) metal coordination : angle 5.36443 / 2.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 196 time to evaluate : 1.564 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: A 89 LEU cc_start: 0.8704 (mt) cc_final: 0.8480 (mt) REVERT: A 166 LYS cc_start: 0.8868 (tppt) cc_final: 0.8584 (tppt) REVERT: A 234 ILE cc_start: 0.9252 (tt) cc_final: 0.8955 (mt) REVERT: A 270 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7616 (pp) REVERT: A 323 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8469 (mm) REVERT: A 386 TRP cc_start: 0.8131 (OUTLIER) cc_final: 0.5555 (p-90) REVERT: A 504 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7945 (mm) REVERT: B 43 MET cc_start: 0.6546 (pmm) cc_final: 0.5701 (pmm) REVERT: B 169 MET cc_start: 0.8597 (tmm) cc_final: 0.8172 (tmm) REVERT: B 232 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7200 (mpp80) REVERT: B 418 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: B 446 PHE cc_start: 0.7154 (OUTLIER) cc_final: 0.6522 (m-80) REVERT: B 460 MET cc_start: 0.8212 (tmm) cc_final: 0.7938 (tmm) REVERT: C 43 MET cc_start: 0.7947 (pmm) cc_final: 0.7671 (pmm) REVERT: C 169 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8261 (ttp) REVERT: D 193 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8465 (m-10) REVERT: D 287 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9014 (mt) REVERT: D 294 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6592 (ptt-90) REVERT: E 172 ILE cc_start: 0.7951 (OUTLIER) cc_final: 0.7715 (pt) REVERT: E 189 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7990 (tp30) REVERT: I 597 LEU cc_start: 0.6640 (OUTLIER) cc_final: 0.6389 (tp) REVERT: J 593 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8351 (m-80) REVERT: J 614 ARG cc_start: 0.7823 (ttt180) cc_final: 0.7447 (ttm-80) REVERT: a 191 ASN cc_start: 0.8516 (t0) cc_final: 0.7889 (m-40) REVERT: a 398 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8892 (mtpt) REVERT: a 481 ASN cc_start: 0.8452 (t0) cc_final: 0.8160 (t0) REVERT: a 533 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8675 (mm) REVERT: b 1 MET cc_start: 0.6631 (ptp) cc_final: 0.6159 (ptt) REVERT: b 328 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6687 (p0) REVERT: b 555 MET cc_start: 0.6055 (mmm) cc_final: 0.4572 (ppp) REVERT: c 43 MET cc_start: -0.0927 (tpt) cc_final: -0.2242 (mmp) REVERT: c 120 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: d 1 MET cc_start: 0.4812 (ttt) cc_final: 0.3837 (tpp) REVERT: d 65 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.8389 (m-80) REVERT: d 173 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7385 (m-30) REVERT: d 189 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8035 (pp30) REVERT: e 1 MET cc_start: 0.3431 (tmm) cc_final: 0.2540 (tpt) REVERT: e 27 LEU cc_start: 0.8077 (mt) cc_final: 0.7642 (tt) outliers start: 146 outliers final: 102 residues processed: 326 average time/residue: 0.2308 time to fit residues: 128.3492 Evaluate side-chains 317 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 193 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 335 TYR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain H residue 628 LEU Chi-restraints excluded: chain I residue 597 LEU Chi-restraints excluded: chain I residue 599 VAL Chi-restraints excluded: chain J residue 593 PHE Chi-restraints excluded: chain J residue 599 VAL Chi-restraints excluded: chain a residue 49 TYR Chi-restraints excluded: chain a residue 71 ASN Chi-restraints excluded: chain a residue 75 TYR Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 128 SER Chi-restraints excluded: chain a residue 190 LEU Chi-restraints excluded: chain a residue 215 LEU Chi-restraints excluded: chain a residue 217 ASP Chi-restraints excluded: chain a residue 241 LEU Chi-restraints excluded: chain a residue 297 ILE Chi-restraints excluded: chain a residue 338 PHE Chi-restraints excluded: chain a residue 379 ASN Chi-restraints excluded: chain a residue 395 PHE Chi-restraints excluded: chain a residue 398 LYS Chi-restraints excluded: chain a residue 528 THR Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 111 SER Chi-restraints excluded: chain b residue 121 ASN Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 149 ASP Chi-restraints excluded: chain b residue 154 VAL Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain b residue 233 LEU Chi-restraints excluded: chain b residue 276 LEU Chi-restraints excluded: chain b residue 316 VAL Chi-restraints excluded: chain b residue 320 LEU Chi-restraints excluded: chain b residue 328 ASP Chi-restraints excluded: chain b residue 336 ARG Chi-restraints excluded: chain b residue 360 ASN Chi-restraints excluded: chain b residue 554 GLU Chi-restraints excluded: chain b residue 600 GLU Chi-restraints excluded: chain c residue 32 ASN Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 120 GLU Chi-restraints excluded: chain c residue 382 TYR Chi-restraints excluded: chain c residue 459 VAL Chi-restraints excluded: chain c residue 545 ILE Chi-restraints excluded: chain d residue 65 TYR Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain d residue 165 VAL Chi-restraints excluded: chain d residue 173 ASP Chi-restraints excluded: chain d residue 189 GLN Chi-restraints excluded: chain d residue 254 GLN Chi-restraints excluded: chain d residue 357 LYS Chi-restraints excluded: chain d residue 361 MET Chi-restraints excluded: chain d residue 363 ARG Chi-restraints excluded: chain d residue 454 VAL Chi-restraints excluded: chain d residue 466 ILE Chi-restraints excluded: chain d residue 471 LYS Chi-restraints excluded: chain d residue 478 ILE Chi-restraints excluded: chain e residue 116 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 387 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 421 optimal weight: 8.9990 chunk 443 optimal weight: 20.0000 chunk 253 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 394 optimal weight: 3.9990 chunk 330 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** J 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 327 GLN ** b 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 219 GLN ** c 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.090475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.065239 restraints weight = 223180.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.064950 restraints weight = 119525.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.065477 restraints weight = 76578.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.065898 restraints weight = 57635.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.066313 restraints weight = 48874.160| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 41285 Z= 0.178 Angle : 0.631 11.067 56221 Z= 0.327 Chirality : 0.042 0.366 6189 Planarity : 0.004 0.115 6798 Dihedral : 15.318 179.299 6110 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.04 % Favored : 94.83 % Rotamer: Outliers : 3.91 % Allowed : 26.88 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.42 (0.13), residues: 4548 helix: 1.10 (0.10), residues: 2714 sheet: -0.13 (0.40), residues: 190 loop : -1.01 (0.16), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG b 455 TYR 0.037 0.001 TYR a 49 PHE 0.043 0.002 PHE H 593 TRP 0.035 0.002 TRP c 200 HIS 0.009 0.001 HIS c 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (41279) covalent geometry : angle 0.62765 / 0.33 (56211) SS BOND : bond 0.00462 / 0.22 ( 2) SS BOND : angle 1.88119 / 0.94 ( 4) hydrogen bonds : bond 0.04087 / 2.70 ( 2000) hydrogen bonds : angle 4.41740 / 3.17 ( 5794) metal coordination : bond 0.01469 / 0.75 ( 4) metal coordination : angle 5.89144 / 2.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 194 time to evaluate : 1.544 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: A 166 LYS cc_start: 0.8859 (tppt) cc_final: 0.8572 (tppt) REVERT: A 270 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7937 (pp) REVERT: A 323 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8629 (mm) REVERT: A 386 TRP cc_start: 0.8215 (OUTLIER) cc_final: 0.5700 (p-90) REVERT: A 504 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8101 (mm) REVERT: B 43 MET cc_start: 0.6549 (pmm) cc_final: 0.5789 (pmm) REVERT: B 169 MET cc_start: 0.8589 (tmm) cc_final: 0.8151 (tmm) REVERT: B 232 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7398 (mpp80) REVERT: B 418 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8501 (m-80) REVERT: B 446 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6646 (m-80) REVERT: B 460 MET cc_start: 0.8246 (tmm) cc_final: 0.7876 (tmm) REVERT: C 43 MET cc_start: 0.7991 (pmm) cc_final: 0.7657 (pmm) REVERT: C 169 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8268 (ttp) REVERT: D 193 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8522 (m-10) REVERT: D 287 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8971 (mt) REVERT: D 294 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6676 (ptt-90) REVERT: E 172 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7849 (pt) REVERT: E 189 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7917 (tp30) REVERT: I 604 PHE cc_start: 0.8818 (OUTLIER) cc_final: 0.8601 (t80) REVERT: J 593 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.8134 (m-80) REVERT: J 614 ARG cc_start: 0.8230 (ttt180) cc_final: 0.7745 (ttm-80) REVERT: a 191 ASN cc_start: 0.8660 (t0) cc_final: 0.7876 (m-40) REVERT: a 398 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8939 (mtpt) REVERT: a 481 ASN cc_start: 0.8506 (t0) cc_final: 0.8229 (t0) REVERT: a 533 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8732 (mm) REVERT: b 1 MET cc_start: 0.7181 (ptp) cc_final: 0.6834 (ptt) REVERT: b 103 MET cc_start: 0.3697 (ttp) cc_final: 0.3469 (tpt) REVERT: b 126 TYR cc_start: 0.0789 (OUTLIER) cc_final: -0.0631 (p90) REVERT: b 328 ASP cc_start: 0.6947 (OUTLIER) cc_final: 0.6649 (p0) REVERT: b 555 MET cc_start: 0.6148 (mmm) cc_final: 0.5095 (ppp) REVERT: c 43 MET cc_start: -0.0844 (tpt) cc_final: -0.2080 (mmp) REVERT: c 174 MET cc_start: 0.4773 (tpp) cc_final: 0.4303 (mtt) REVERT: d 1 MET cc_start: 0.4755 (ttt) cc_final: 0.3744 (tpp) REVERT: d 65 TYR cc_start: 0.8890 (OUTLIER) cc_final: 0.8438 (m-80) REVERT: d 173 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7374 (m-30) REVERT: d 189 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8052 (pp30) REVERT: e 1 MET cc_start: 0.4115 (tmm) cc_final: 0.3656 (tpt) REVERT: e 27 LEU cc_start: 0.8118 (mt) cc_final: 0.7724 (tt) outliers start: 169 outliers final: 114 residues processed: 345 average time/residue: 0.2135 time to fit residues: 124.1046 Evaluate side-chains 314 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 178 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 335 TYR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain H residue 628 LEU Chi-restraints excluded: chain I residue 599 VAL Chi-restraints excluded: chain I residue 604 PHE Chi-restraints excluded: chain J residue 593 PHE Chi-restraints excluded: chain J residue 599 VAL Chi-restraints excluded: chain a residue 49 TYR Chi-restraints excluded: chain a residue 71 ASN Chi-restraints excluded: chain a residue 75 TYR Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 128 SER Chi-restraints excluded: chain a residue 190 LEU Chi-restraints excluded: chain a residue 215 LEU Chi-restraints excluded: chain a residue 217 ASP Chi-restraints excluded: chain a residue 241 LEU Chi-restraints excluded: chain a residue 297 ILE Chi-restraints excluded: chain a residue 338 PHE Chi-restraints excluded: chain a residue 339 SER Chi-restraints excluded: chain a residue 379 ASN Chi-restraints excluded: chain a residue 395 PHE Chi-restraints excluded: chain a residue 398 LYS Chi-restraints excluded: chain a residue 484 ILE Chi-restraints excluded: chain a residue 528 THR Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain a residue 535 ILE Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 111 SER Chi-restraints excluded: chain b residue 121 ASN Chi-restraints excluded: chain b residue 126 TYR Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 149 ASP Chi-restraints excluded: chain b residue 154 VAL Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain b residue 233 LEU Chi-restraints excluded: chain b residue 316 VAL Chi-restraints excluded: chain b residue 328 ASP Chi-restraints excluded: chain b residue 336 ARG Chi-restraints excluded: chain b residue 360 ASN Chi-restraints excluded: chain b residue 554 GLU Chi-restraints excluded: chain b residue 600 GLU Chi-restraints excluded: chain c residue 32 ASN Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 186 TYR Chi-restraints excluded: chain c residue 382 TYR Chi-restraints excluded: chain c residue 459 VAL Chi-restraints excluded: chain c residue 477 VAL Chi-restraints excluded: chain c residue 545 ILE Chi-restraints excluded: chain d residue 65 TYR Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain d residue 165 VAL Chi-restraints excluded: chain d residue 173 ASP Chi-restraints excluded: chain d residue 189 GLN Chi-restraints excluded: chain d residue 257 SER Chi-restraints excluded: chain d residue 357 LYS Chi-restraints excluded: chain d residue 361 MET Chi-restraints excluded: chain d residue 363 ARG Chi-restraints excluded: chain d residue 450 ASN Chi-restraints excluded: chain d residue 454 VAL Chi-restraints excluded: chain d residue 466 ILE Chi-restraints excluded: chain d residue 471 LYS Chi-restraints excluded: chain d residue 478 ILE Chi-restraints excluded: chain e residue 116 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 7.9990 chunk 390 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 400 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 449 optimal weight: 6.9990 chunk 333 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 ASN B 110 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN B 262 HIS B 454 ASN ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN D 407 HIS E 101 ASN E 174 ASN E 188 ASN H 620 GLN ** J 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 57 GLN ** a 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 521 ASN ** b 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 327 GLN ** b 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 74 ASN c 303 GLN ** c 447 HIS ** 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 = 0.4104 r_free = 0.4104 target = 0.088038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.062364 restraints weight = 220341.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.062460 restraints weight = 127774.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.062985 restraints weight = 80372.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.062950 restraints weight = 58668.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.062975 restraints weight = 52699.991| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 41285 Z= 0.299 Angle : 0.757 13.987 56221 Z= 0.390 Chirality : 0.046 0.383 6189 Planarity : 0.005 0.120 6798 Dihedral : 15.493 177.701 6106 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.83 % Favored : 94.04 % Rotamer: Outliers : 3.93 % Allowed : 26.91 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.01 (0.12), residues: 4548 helix: 0.73 (0.10), residues: 2740 sheet: -0.20 (0.40), residues: 181 loop : -1.19 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG b 455 TYR 0.035 0.002 TYR a 49 PHE 0.047 0.002 PHE H 593 TRP 0.059 0.003 TRP e 93 HIS 0.015 0.002 HIS e 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.30 (41279) covalent geometry : angle 0.75229 / 0.39 (56211) SS BOND : bond 0.00860 / 0.41 ( 2) SS BOND : angle 2.14707 / 1.09 ( 4) hydrogen bonds : bond 0.04712 / 3.15 ( 2000) hydrogen bonds : angle 4.73705 / 3.39 ( 5794) metal coordination : bond 0.02186 / 1.11 ( 4) metal coordination : angle 8.14127 / 4.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 178 time to evaluate : 1.295 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: A 166 LYS cc_start: 0.8868 (tppt) cc_final: 0.8623 (tppt) REVERT: A 270 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8028 (pp) REVERT: A 323 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8635 (mm) REVERT: A 386 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.5754 (p-90) REVERT: A 504 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7972 (mm) REVERT: B 43 MET cc_start: 0.7117 (pmm) cc_final: 0.6228 (pmm) REVERT: B 110 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8152 (mp10) REVERT: B 169 MET cc_start: 0.8652 (tmm) cc_final: 0.8211 (tmm) REVERT: B 232 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7591 (mpp80) REVERT: B 418 TYR cc_start: 0.9214 (OUTLIER) cc_final: 0.8791 (m-10) REVERT: B 446 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7026 (m-80) REVERT: B 473 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.8701 (t80) REVERT: C 43 MET cc_start: 0.8210 (pmm) cc_final: 0.7725 (pmm) REVERT: C 169 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8276 (ttp) REVERT: C 208 MET cc_start: 0.8354 (tpp) cc_final: 0.7734 (tpp) REVERT: D 193 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8553 (m-10) REVERT: D 287 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9007 (mm) REVERT: D 294 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.6797 (ptt-90) REVERT: E 172 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8108 (pt) REVERT: E 181 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: E 189 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8088 (tp30) REVERT: J 593 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: J 609 MET cc_start: 0.6438 (tpp) cc_final: 0.5826 (tpp) REVERT: J 614 ARG cc_start: 0.7887 (ttt180) cc_final: 0.7371 (ttm-80) REVERT: a 398 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8986 (mtpt) REVERT: a 481 ASN cc_start: 0.8495 (t0) cc_final: 0.8246 (t0) REVERT: a 533 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8972 (mm) REVERT: b 1 MET cc_start: 0.7111 (ptp) cc_final: 0.6623 (ptp) REVERT: b 103 MET cc_start: 0.3900 (ttp) cc_final: 0.3616 (tpt) REVERT: b 126 TYR cc_start: 0.1441 (OUTLIER) cc_final: -0.0141 (p90) REVERT: b 328 ASP cc_start: 0.6749 (OUTLIER) cc_final: 0.6408 (p0) REVERT: c 197 ARG cc_start: 0.5024 (OUTLIER) cc_final: 0.4052 (ptt180) REVERT: d 1 MET cc_start: 0.5131 (ttt) cc_final: 0.4071 (tpp) REVERT: d 65 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8603 (m-80) REVERT: d 173 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7244 (m-30) REVERT: d 387 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7525 (t80) REVERT: e 1 MET cc_start: 0.4641 (tmm) cc_final: 0.4314 (tpt) REVERT: e 27 LEU cc_start: 0.8211 (mt) cc_final: 0.7803 (tt) outliers start: 170 outliers final: 124 residues processed: 330 average time/residue: 0.2128 time to fit residues: 118.8979 Evaluate side-chains 321 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 172 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 GLN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 335 TYR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 256 THR Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 403 PHE Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 448 VAL Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain H residue 593 PHE Chi-restraints excluded: chain H residue 616 TYR Chi-restraints excluded: chain H residue 628 LEU Chi-restraints excluded: chain I residue 599 VAL Chi-restraints excluded: chain J residue 593 PHE Chi-restraints excluded: chain J residue 599 VAL Chi-restraints excluded: chain J residue 621 LEU Chi-restraints excluded: chain a residue 49 TYR Chi-restraints excluded: chain a residue 71 ASN Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 75 TYR Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 128 SER Chi-restraints excluded: chain a residue 190 LEU Chi-restraints excluded: chain a residue 215 LEU Chi-restraints excluded: chain a residue 217 ASP Chi-restraints excluded: chain a residue 241 LEU Chi-restraints excluded: chain a residue 297 ILE Chi-restraints excluded: chain a residue 338 PHE Chi-restraints excluded: chain a residue 339 SER Chi-restraints excluded: chain a residue 379 ASN Chi-restraints excluded: chain a residue 398 LYS Chi-restraints excluded: chain a residue 414 THR Chi-restraints excluded: chain a residue 484 ILE Chi-restraints excluded: chain a residue 489 ILE Chi-restraints excluded: chain a residue 528 THR Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 111 SER Chi-restraints excluded: chain b residue 121 ASN Chi-restraints excluded: chain b residue 126 TYR Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 149 ASP Chi-restraints excluded: chain b residue 154 VAL Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain b residue 233 LEU Chi-restraints excluded: chain b residue 314 THR Chi-restraints excluded: chain b residue 316 VAL Chi-restraints excluded: chain b residue 320 LEU Chi-restraints excluded: chain b residue 328 ASP Chi-restraints excluded: chain b residue 336 ARG Chi-restraints excluded: chain b residue 360 ASN Chi-restraints excluded: chain b residue 554 GLU Chi-restraints excluded: chain c residue 32 ASN Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 115 MET Chi-restraints excluded: chain c residue 186 TYR Chi-restraints excluded: chain c residue 197 ARG Chi-restraints excluded: chain c residue 382 TYR Chi-restraints excluded: chain c residue 459 VAL Chi-restraints excluded: chain c residue 477 VAL Chi-restraints excluded: chain c residue 545 ILE Chi-restraints excluded: chain c residue 555 MET Chi-restraints excluded: chain d residue 41 LYS Chi-restraints excluded: chain d residue 65 TYR Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain d residue 165 VAL Chi-restraints excluded: chain d residue 173 ASP Chi-restraints excluded: chain d residue 257 SER Chi-restraints excluded: chain d residue 361 MET Chi-restraints excluded: chain d residue 363 ARG Chi-restraints excluded: chain d residue 387 PHE Chi-restraints excluded: chain d residue 450 ASN Chi-restraints excluded: chain d residue 454 VAL Chi-restraints excluded: chain d residue 466 ILE Chi-restraints excluded: chain d residue 471 LYS Chi-restraints excluded: chain e residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 128 optimal weight: 1.9990 chunk 288 optimal weight: 0.5980 chunk 379 optimal weight: 5.9990 chunk 376 optimal weight: 7.9990 chunk 367 optimal weight: 9.9990 chunk 256 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 444 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.0020 overall best weight: 1.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 395 ASN ** c 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.089862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.063772 restraints weight = 209418.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.063038 restraints weight = 122877.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.063314 restraints weight = 78470.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.063465 restraints weight = 58461.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.063589 restraints weight = 52176.953| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 41285 Z= 0.137 Angle : 0.643 12.746 56221 Z= 0.331 Chirality : 0.043 0.395 6189 Planarity : 0.004 0.117 6798 Dihedral : 15.381 174.704 6106 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.08 % Favored : 94.81 % Rotamer: Outliers : 2.75 % Allowed : 27.99 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.30 (0.13), residues: 4548 helix: 1.01 (0.10), residues: 2709 sheet: -0.13 (0.42), residues: 173 loop : -1.05 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 455 TYR 0.037 0.001 TYR a 49 PHE 0.047 0.002 PHE H 593 TRP 0.039 0.002 TRP c 200 HIS 0.022 0.001 HIS B 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (41279) covalent geometry : angle 0.63908 / 0.33 (56211) SS BOND : bond 0.00503 / 0.24 ( 2) SS BOND : angle 1.76144 / 0.89 ( 4) hydrogen bonds : bond 0.04071 / 2.67 ( 2000) hydrogen bonds : angle 4.45774 / 3.20 ( 5794) metal coordination : bond 0.01205 / 0.63 ( 4) metal coordination : angle 6.97749 / 3.51 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9096 Ramachandran restraints generated. 4548 Oldfield, 0 Emsley, 4548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 190 time to evaluate : 1.526 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: A 166 LYS cc_start: 0.8869 (tppt) cc_final: 0.8599 (tppt) REVERT: A 270 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7899 (pp) REVERT: A 323 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8489 (mm) REVERT: A 386 TRP cc_start: 0.8083 (OUTLIER) cc_final: 0.5725 (p-90) REVERT: A 504 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7988 (mm) REVERT: B 43 MET cc_start: 0.6721 (pmm) cc_final: 0.5792 (pmm) REVERT: B 169 MET cc_start: 0.8652 (tmm) cc_final: 0.8280 (tmm) REVERT: B 232 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7498 (mpp80) REVERT: B 418 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.8363 (m-10) REVERT: B 446 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.6865 (m-80) REVERT: C 43 MET cc_start: 0.8146 (pmm) cc_final: 0.7686 (pmm) REVERT: C 169 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8301 (ttp) REVERT: C 208 MET cc_start: 0.8105 (tpp) cc_final: 0.7435 (tpp) REVERT: D 193 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8354 (m-10) REVERT: D 287 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9071 (mm) REVERT: D 294 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6822 (ptt-90) REVERT: D 361 MET cc_start: 0.8162 (mpp) cc_final: 0.7014 (mtm) REVERT: E 172 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7717 (pt) REVERT: E 189 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8012 (tp30) REVERT: J 593 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8402 (m-80) REVERT: J 609 MET cc_start: 0.6131 (tpp) cc_final: 0.5478 (tpp) REVERT: J 614 ARG cc_start: 0.7775 (ttt180) cc_final: 0.7306 (ttm-80) REVERT: a 398 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8972 (mtpt) REVERT: a 481 ASN cc_start: 0.8425 (t0) cc_final: 0.8159 (t0) REVERT: a 533 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8915 (mm) REVERT: b 1 MET cc_start: 0.7240 (ptp) cc_final: 0.6910 (ptp) REVERT: b 103 MET cc_start: 0.3693 (ttp) cc_final: 0.3487 (tpt) REVERT: b 126 TYR cc_start: 0.0644 (OUTLIER) cc_final: -0.0779 (p90) REVERT: b 328 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6695 (p0) REVERT: b 555 MET cc_start: 0.6110 (mmm) cc_final: 0.5117 (ppp) REVERT: c 43 MET cc_start: -0.0244 (tpt) cc_final: -0.1377 (mmp) REVERT: c 174 MET cc_start: 0.4557 (tpp) cc_final: 0.4056 (mtt) REVERT: c 197 ARG cc_start: 0.4978 (OUTLIER) cc_final: 0.4157 (ptt180) REVERT: d 1 MET cc_start: 0.5386 (ttt) cc_final: 0.4310 (tpp) REVERT: d 65 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.8433 (m-80) REVERT: d 173 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7231 (m-30) REVERT: e 1 MET cc_start: 0.5243 (tmm) cc_final: 0.5004 (tpt) REVERT: e 27 LEU cc_start: 0.8180 (mt) cc_final: 0.7842 (tt) outliers start: 119 outliers final: 83 residues processed: 299 average time/residue: 0.2325 time to fit residues: 118.2668 Evaluate side-chains 287 residues out of total 4330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 183 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 386 TRP Chi-restraints excluded: chain A residue 504 ILE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 208 MET Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 232 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 446 PHE Chi-restraints excluded: chain B residue 454 ASN Chi-restraints excluded: chain B residue 523 LYS Chi-restraints excluded: chain B residue 531 ASP Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 126 TYR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 169 MET Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 335 TYR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 479 SER Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 294 ARG Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain H residue 628 LEU Chi-restraints excluded: chain I residue 599 VAL Chi-restraints excluded: chain J residue 593 PHE Chi-restraints excluded: chain J residue 599 VAL Chi-restraints excluded: chain a residue 49 TYR Chi-restraints excluded: chain a residue 71 ASN Chi-restraints excluded: chain a residue 75 TYR Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 215 LEU Chi-restraints excluded: chain a residue 241 LEU Chi-restraints excluded: chain a residue 338 PHE Chi-restraints excluded: chain a residue 339 SER Chi-restraints excluded: chain a residue 395 PHE Chi-restraints excluded: chain a residue 398 LYS Chi-restraints excluded: chain a residue 414 THR Chi-restraints excluded: chain a residue 528 THR Chi-restraints excluded: chain a residue 533 LEU Chi-restraints excluded: chain b residue 121 ASN Chi-restraints excluded: chain b residue 126 TYR Chi-restraints excluded: chain b residue 134 SER Chi-restraints excluded: chain b residue 149 ASP Chi-restraints excluded: chain b residue 154 VAL Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain b residue 233 LEU Chi-restraints excluded: chain b residue 316 VAL Chi-restraints excluded: chain b residue 328 ASP Chi-restraints excluded: chain b residue 360 ASN Chi-restraints excluded: chain b residue 554 GLU Chi-restraints excluded: chain c residue 32 ASN Chi-restraints excluded: chain c residue 109 ASP Chi-restraints excluded: chain c residue 186 TYR Chi-restraints excluded: chain c residue 197 ARG Chi-restraints excluded: chain c residue 382 TYR Chi-restraints excluded: chain c residue 459 VAL Chi-restraints excluded: chain c residue 477 VAL Chi-restraints excluded: chain c residue 545 ILE Chi-restraints excluded: chain d residue 65 TYR Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 143 THR Chi-restraints excluded: chain d residue 165 VAL Chi-restraints excluded: chain d residue 173 ASP Chi-restraints excluded: chain d residue 257 SER Chi-restraints excluded: chain d residue 361 MET Chi-restraints excluded: chain d residue 363 ARG Chi-restraints excluded: chain d residue 454 VAL Chi-restraints excluded: chain d residue 466 ILE Chi-restraints excluded: chain d residue 471 LYS Chi-restraints excluded: chain d residue 478 ILE Chi-restraints excluded: chain e residue 116 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 316 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 408 optimal weight: 7.9990 chunk 308 optimal weight: 0.3980 chunk 348 optimal weight: 7.9990 chunk 282 optimal weight: 7.9990 chunk 310 optimal weight: 2.9990 chunk 245 optimal weight: 0.9980 chunk 236 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 230 optimal weight: 7.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN ** B 456 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.089292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.064169 restraints weight = 223793.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.063782 restraints weight = 121271.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.064355 restraints weight = 77668.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.064752 restraints weight = 58886.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.065034 restraints weight = 49645.489| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 41285 Z= 0.205 Angle : 0.668 12.552 56221 Z= 0.344 Chirality : 0.043 0.397 6189 Planarity : 0.004 0.118 6798 Dihedral : 15.414 173.219 6104 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.39 % Favored : 94.50 % Rotamer: Outliers : 2.89 % Allowed : 27.85 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.22 (0.13), residues: 4548 helix: 0.94 (0.10), residues: 2732 sheet: -0.10 (0.41), residues: 180 loop : -1.12 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 262 TYR 0.036 0.002 TYR a 49 PHE 0.049 0.002 PHE H 593 TRP 0.038 0.002 TRP c 200 HIS 0.014 0.001 HIS B 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (41279) covalent geometry : angle 0.66435 / 0.34 (56211) SS BOND : bond 0.00636 / 0.30 ( 2) SS BOND : angle 1.78779 / 0.90 ( 4) hydrogen bonds : bond 0.04183 / 2.76 ( 2000) hydrogen bonds : angle 4.53739 / 3.26 ( 5794) metal coordination : bond 0.01591 / 0.81 ( 4) metal coordination : angle 6.93976 / 3.44 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10051.99 seconds wall clock time: 173 minutes 32.58 seconds (10412.58 seconds total)