Starting phenix.real_space_refine on Sat Mar 7 09:09:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fde_31541/03_2026/7fde_31541.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fde_31541/03_2026/7fde_31541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fde_31541/03_2026/7fde_31541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fde_31541/03_2026/7fde_31541.map" model { file = "/net/cci-nas-00/data/ceres_data/7fde_31541/03_2026/7fde_31541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fde_31541/03_2026/7fde_31541.cif" } resolution = 3.8 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= 0.129 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1210 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 25046 2.51 5 N 6704 2.21 5 O 7681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39557 Number of models: 1 Model: "" Number of chains: 16 Chain: "O" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2878 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 347} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 1833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1833 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 224} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 876 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "A" Number of atoms: 4587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4587 Classifications: {'peptide': 594} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 563} Chain: "B" Number of atoms: 3706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3706 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain breaks: 1 Chain: "C" Number of atoms: 4587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4587 Classifications: {'peptide': 594} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 563} Chain: "D" Number of atoms: 3681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3681 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 442} Chain breaks: 1 Chain: "E" Number of atoms: 4587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4587 Classifications: {'peptide': 594} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 563} Chain: "F" Number of atoms: 3699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3699 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 444} Chain breaks: 1 Chain: "K" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1613 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain: "L" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "M" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 3, 'TRANS': 214} Chain: "N" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 928 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "I" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1801 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 876 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 1, 'TRANS': 110} Chain: "P" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1418 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 7.95, per 1000 atoms: 0.20 Number of scatterers: 39557 At special positions: 0 Unit cell: (147.96, 154.44, 189, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 7681 8.00 N 6704 7.00 C 25046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.6 seconds 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9416 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 54 sheets defined 50.4% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'O' and resid 29 through 36 Processing helix chain 'O' and resid 60 through 89 Processing helix chain 'O' and resid 101 through 105 Processing helix chain 'O' and resid 106 through 113 removed outlier: 3.570A pdb=" N GLU O 112 " --> pdb=" O PRO O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 167 Processing helix chain 'O' and resid 180 through 184 Processing helix chain 'O' and resid 202 through 208 Processing helix chain 'O' and resid 210 through 214 removed outlier: 3.736A pdb=" N LEU O 213 " --> pdb=" O TYR O 210 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER O 214 " --> pdb=" O GLU O 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 210 through 214' Processing helix chain 'O' and resid 241 through 253 removed outlier: 4.088A pdb=" N GLU O 245 " --> pdb=" O LYS O 241 " (cutoff:3.500A) Processing helix chain 'O' and resid 265 through 319 removed outlier: 3.517A pdb=" N GLN O 269 " --> pdb=" O GLU O 265 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN O 282 " --> pdb=" O ALA O 278 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG O 285 " --> pdb=" O GLU O 281 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE O 300 " --> pdb=" O TYR O 296 " (cutoff:3.500A) Processing helix chain 'O' and resid 336 through 349 Processing helix chain 'O' and resid 350 through 353 Processing helix chain 'G' and resid 11 through 111 removed outlier: 3.849A pdb=" N LYS G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU G 102 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR G 103 " --> pdb=" O ILE G 99 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS G 104 " --> pdb=" O PHE G 100 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU G 105 " --> pdb=" O GLU G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 133 Proline residue: G 119 - end of helix Processing helix chain 'G' and resid 145 through 164 removed outlier: 4.142A pdb=" N ASP G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASP G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 211 Processing helix chain 'G' and resid 214 through 223 Processing helix chain 'H' and resid 3 through 5 No H-bonds generated for 'chain 'H' and resid 3 through 5' Processing helix chain 'H' and resid 6 through 63 removed outlier: 3.883A pdb=" N LEU H 10 " --> pdb=" O GLY H 6 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN H 61 " --> pdb=" O PHE H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 76 removed outlier: 4.158A pdb=" N GLU H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 90 removed outlier: 3.521A pdb=" N LYS H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 104 Processing helix chain 'A' and resid 111 through 120 removed outlier: 3.519A pdb=" N ILE A 115 " --> pdb=" O PRO A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 244 removed outlier: 4.015A pdb=" N ASP A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 331 through 346 removed outlier: 3.566A pdb=" N GLN A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 383 through 394 Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 443 through 449 removed outlier: 3.759A pdb=" N GLN A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 475 removed outlier: 4.547A pdb=" N LYS A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N PHE A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 503 removed outlier: 3.607A pdb=" N GLN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 507 Processing helix chain 'A' and resid 508 through 525 Processing helix chain 'A' and resid 539 through 563 removed outlier: 3.510A pdb=" N THR A 543 " --> pdb=" O PRO A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 574 through 585 removed outlier: 4.064A pdb=" N LYS A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 616 Processing helix chain 'B' and resid 10 through 20 removed outlier: 3.731A pdb=" N LYS B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 removed outlier: 3.551A pdb=" N MET B 108 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 105 through 109' Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 155 through 163 removed outlier: 4.120A pdb=" N MET B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 163 " --> pdb=" O ASP B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.732A pdb=" N GLU B 236 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 271 Proline residue: B 256 - end of helix Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 305 through 306 No H-bonds generated for 'chain 'B' and resid 305 through 306' Processing helix chain 'B' and resid 307 through 317 removed outlier: 3.795A pdb=" N ASP B 311 " --> pdb=" O TYR B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 361 through 367 removed outlier: 3.611A pdb=" N HIS B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 386 Processing helix chain 'B' and resid 395 through 420 removed outlier: 3.551A pdb=" N ASN B 401 " --> pdb=" O GLY B 397 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 443 Processing helix chain 'B' and resid 453 through 466 Processing helix chain 'B' and resid 477 through 485 Processing helix chain 'C' and resid 111 through 120 removed outlier: 3.753A pdb=" N ILE C 115 " --> pdb=" O PRO C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 244 Processing helix chain 'C' and resid 261 through 273 removed outlier: 3.843A pdb=" N SER C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N GLN C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 297 removed outlier: 3.735A pdb=" N ALA C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'C' and resid 325 through 346 removed outlier: 3.885A pdb=" N ALA C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TYR C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C 346 " --> pdb=" O TYR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 372 Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 425 through 435 removed outlier: 3.571A pdb=" N THR C 429 " --> pdb=" O ASP C 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 434 " --> pdb=" O ALA C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 463 through 475 removed outlier: 3.755A pdb=" N ASN C 468 " --> pdb=" O THR C 464 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN C 474 " --> pdb=" O PHE C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 503 removed outlier: 3.743A pdb=" N VAL C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 500 " --> pdb=" O GLU C 496 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU C 501 " --> pdb=" O GLN C 497 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 502 " --> pdb=" O VAL C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 525 Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.507A pdb=" N ALA C 536 " --> pdb=" O THR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 563 Processing helix chain 'C' and resid 566 through 584 removed outlier: 3.673A pdb=" N ASP C 572 " --> pdb=" O SER C 568 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ASP C 576 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL C 577 " --> pdb=" O SER C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 587 No H-bonds generated for 'chain 'C' and resid 585 through 587' Processing helix chain 'C' and resid 594 through 616 Processing helix chain 'D' and resid 10 through 17 Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 105 through 109 removed outlier: 4.189A pdb=" N LEU D 109 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 179 through 191 Processing helix chain 'D' and resid 218 through 233 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 250 through 253 Processing helix chain 'D' and resid 254 through 270 Processing helix chain 'D' and resid 280 through 291 removed outlier: 3.738A pdb=" N TYR D 284 " --> pdb=" O ASP D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 306 No H-bonds generated for 'chain 'D' and resid 305 through 306' Processing helix chain 'D' and resid 307 through 318 removed outlier: 4.430A pdb=" N ARG D 318 " --> pdb=" O THR D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 354 Processing helix chain 'D' and resid 361 through 367 removed outlier: 3.770A pdb=" N HIS D 365 " --> pdb=" O ASP D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 387 Processing helix chain 'D' and resid 395 through 418 removed outlier: 3.786A pdb=" N SER D 400 " --> pdb=" O HIS D 396 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASN D 401 " --> pdb=" O GLY D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 443 removed outlier: 3.504A pdb=" N GLU D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 466 Processing helix chain 'D' and resid 477 through 486 removed outlier: 3.920A pdb=" N ASP D 486 " --> pdb=" O ASP D 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 120 removed outlier: 3.834A pdb=" N ILE E 115 " --> pdb=" O PRO E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 244 Processing helix chain 'E' and resid 262 through 273 Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.694A pdb=" N ALA E 291 " --> pdb=" O GLY E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 346 removed outlier: 3.821A pdb=" N ALA E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE E 333 " --> pdb=" O ARG E 329 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR E 334 " --> pdb=" O GLU E 330 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN E 346 " --> pdb=" O TYR E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 372 removed outlier: 4.252A pdb=" N TRP E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 380 Processing helix chain 'E' and resid 383 through 394 removed outlier: 3.783A pdb=" N ARG E 394 " --> pdb=" O SER E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 433 Processing helix chain 'E' and resid 443 through 448 Processing helix chain 'E' and resid 467 through 475 removed outlier: 3.885A pdb=" N SER E 473 " --> pdb=" O LYS E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 503 removed outlier: 4.308A pdb=" N GLN E 497 " --> pdb=" O GLU E 493 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 507 Processing helix chain 'E' and resid 508 through 525 Processing helix chain 'E' and resid 539 through 565 removed outlier: 3.959A pdb=" N ALA E 565 " --> pdb=" O VAL E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 575 removed outlier: 4.022A pdb=" N ASP E 572 " --> pdb=" O SER E 568 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER E 573 " --> pdb=" O LYS E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 584 removed outlier: 3.536A pdb=" N HIS E 579 " --> pdb=" O GLY E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 585 through 587 No H-bonds generated for 'chain 'E' and resid 585 through 587' Processing helix chain 'E' and resid 594 through 614 Processing helix chain 'F' and resid 10 through 15 removed outlier: 3.536A pdb=" N ALA F 15 " --> pdb=" O ILE F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 20 removed outlier: 3.924A pdb=" N PHE F 20 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 109 removed outlier: 3.758A pdb=" N LEU F 109 " --> pdb=" O GLU F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 142 No H-bonds generated for 'chain 'F' and resid 140 through 142' Processing helix chain 'F' and resid 155 through 162 removed outlier: 3.902A pdb=" N MET F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'F' and resid 218 through 232 removed outlier: 3.539A pdb=" N ASN F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 238 Processing helix chain 'F' and resid 249 through 253 Processing helix chain 'F' and resid 254 through 270 Processing helix chain 'F' and resid 280 through 294 removed outlier: 3.523A pdb=" N TYR F 284 " --> pdb=" O ASP F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 317 Processing helix chain 'F' and resid 344 through 354 Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 382 through 387 Processing helix chain 'F' and resid 395 through 421 Processing helix chain 'F' and resid 426 through 443 Processing helix chain 'F' and resid 453 through 466 removed outlier: 3.600A pdb=" N SER F 463 " --> pdb=" O ASP F 459 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU F 464 " --> pdb=" O GLN F 460 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU F 465 " --> pdb=" O ALA F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 485 Processing helix chain 'K' and resid 32 through 50 Processing helix chain 'K' and resid 51 through 111 removed outlier: 3.734A pdb=" N LYS K 63 " --> pdb=" O ASP K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 133 Proline residue: K 119 - end of helix removed outlier: 3.810A pdb=" N LYS K 131 " --> pdb=" O GLU K 127 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU K 132 " --> pdb=" O ALA K 128 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU K 133 " --> pdb=" O LEU K 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 152 removed outlier: 3.619A pdb=" N MET K 152 " --> pdb=" O LEU K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 164 Processing helix chain 'K' and resid 203 through 214 Processing helix chain 'K' and resid 214 through 223 Processing helix chain 'L' and resid 22 through 64 removed outlier: 3.556A pdb=" N LYS L 36 " --> pdb=" O LEU L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 75 removed outlier: 3.586A pdb=" N LYS L 70 " --> pdb=" O GLY L 66 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY L 75 " --> pdb=" O LYS L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 90 Processing helix chain 'L' and resid 90 through 103 removed outlier: 4.177A pdb=" N VAL L 94 " --> pdb=" O LYS L 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 75 removed outlier: 3.848A pdb=" N ASP M 45 " --> pdb=" O LYS M 41 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG M 59 " --> pdb=" O GLN M 55 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN M 62 " --> pdb=" O GLY M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 86 Processing helix chain 'M' and resid 126 through 140 removed outlier: 3.867A pdb=" N GLN M 130 " --> pdb=" O GLY M 126 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN M 131 " --> pdb=" O ARG M 127 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN M 133 " --> pdb=" O GLY M 129 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU M 137 " --> pdb=" O GLN M 133 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE M 138 " --> pdb=" O ARG M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 221 removed outlier: 4.031A pdb=" N THR M 145 " --> pdb=" O ARG M 141 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE M 178 " --> pdb=" O GLU M 174 " (cutoff:3.500A) Proline residue: M 179 - end of helix removed outlier: 3.879A pdb=" N ASP M 196 " --> pdb=" O LEU M 192 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG M 197 " --> pdb=" O ASP M 193 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU M 198 " --> pdb=" O GLU M 194 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU M 220 " --> pdb=" O LYS M 216 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N MET M 221 " --> pdb=" O LEU M 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 24 Processing helix chain 'N' and resid 46 through 59 Processing helix chain 'N' and resid 71 through 77 removed outlier: 3.618A pdb=" N ASN N 76 " --> pdb=" O HIS N 72 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE N 77 " --> pdb=" O ILE N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 77 through 84 removed outlier: 3.554A pdb=" N PHE N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 114 Processing helix chain 'I' and resid 8 through 87 removed outlier: 4.038A pdb=" N GLN I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN I 57 " --> pdb=" O ASN I 53 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET I 70 " --> pdb=" O LEU I 66 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN I 73 " --> pdb=" O ALA I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 113 removed outlier: 3.603A pdb=" N ASN I 112 " --> pdb=" O SER I 108 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 133 removed outlier: 3.869A pdb=" N ILE I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 144 No H-bonds generated for 'chain 'I' and resid 142 through 144' Processing helix chain 'I' and resid 145 through 152 removed outlier: 3.684A pdb=" N MET I 152 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 164 Processing helix chain 'I' and resid 202 through 214 removed outlier: 4.429A pdb=" N GLU I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU I 213 " --> pdb=" O LEU I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 224 Processing helix chain 'J' and resid 3 through 61 removed outlier: 4.283A pdb=" N ASP J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER J 45 " --> pdb=" O LYS J 41 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU J 53 " --> pdb=" O GLN J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 65 removed outlier: 3.694A pdb=" N VAL J 65 " --> pdb=" O ALA J 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 62 through 65' Processing helix chain 'J' and resid 66 through 104 removed outlier: 3.957A pdb=" N ALA J 81 " --> pdb=" O GLN J 77 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL J 94 " --> pdb=" O LYS J 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 85 Processing helix chain 'P' and resid 110 through 118 Processing sheet with id=AA1, first strand: chain 'O' and resid 45 through 47 Processing sheet with id=AA2, first strand: chain 'O' and resid 223 through 227 removed outlier: 3.810A pdb=" N SER O 223 " --> pdb=" O ASN O 235 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU O 233 " --> pdb=" O ILE O 225 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU O 227 " --> pdb=" O TYR O 231 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N TYR O 231 " --> pdb=" O GLU O 227 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE O 256 " --> pdb=" O ALA O 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 173 through 174 removed outlier: 3.675A pdb=" N VAL G 189 " --> pdb=" O LYS G 140 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL G 188 " --> pdb=" O ASN G 201 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL G 190 " --> pdb=" O ILE G 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA5, first strand: chain 'A' and resid 29 through 31 removed outlier: 4.050A pdb=" N ARG A 62 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLN A 71 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL A 60 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 93 through 96 Processing sheet with id=AA7, first strand: chain 'A' and resid 104 through 105 removed outlier: 6.749A pdb=" N ILE A 278 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL A 318 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TYR A 280 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 152 removed outlier: 6.683A pdb=" N GLU A 199 " --> pdb=" O THR A 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 225 through 227 removed outlier: 4.106A pdb=" N GLU A 225 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS A 397 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 396 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 398 " --> pdb=" O GLY A 408 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 232 through 233 removed outlier: 4.364A pdb=" N CYS A 246 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 26 through 28 removed outlier: 5.779A pdb=" N ILE I 197 " --> pdb=" O ASN I 192 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL I 188 " --> pdb=" O ASN I 201 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA I 137 " --> pdb=" O GLU I 171 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.887A pdb=" N ALA B 75 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN B 78 " --> pdb=" O GLN B 66 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AB6, first strand: chain 'B' and resid 101 through 104 Processing sheet with id=AB7, first strand: chain 'B' and resid 112 through 113 removed outlier: 8.471A pdb=" N PHE B 241 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N PHE B 212 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N ILE B 332 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR B 276 " --> pdb=" O ILE B 332 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 150 through 151 removed outlier: 4.388A pdb=" N ILE B 164 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 25 through 31 removed outlier: 5.839A pdb=" N ILE C 27 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLU C 38 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 37 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LYS C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE C 63 " --> pdb=" O LYS C 67 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR C 69 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 86 " --> pdb=" O LYS C 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.664A pdb=" N VAL C 94 " --> pdb=" O TRP C 215 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TRP C 215 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 170 through 173 removed outlier: 4.471A pdb=" N GLY C 159 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 151 through 152 removed outlier: 6.594A pdb=" N GLU C 199 " --> pdb=" O THR C 183 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 225 through 226 removed outlier: 3.808A pdb=" N GLU C 225 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 232 through 233 removed outlier: 4.643A pdb=" N CYS C 246 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 278 through 285 removed outlier: 3.585A pdb=" N THR C 316 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR C 280 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY C 284 " --> pdb=" O ASN C 320 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 302 through 303 Processing sheet with id=AC8, first strand: chain 'C' and resid 349 through 350 Processing sheet with id=AC9, first strand: chain 'D' and resid 27 through 28 Processing sheet with id=AD1, first strand: chain 'D' and resid 31 through 35 removed outlier: 5.635A pdb=" N ILE D 40 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N VAL D 34 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU D 38 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA D 75 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE D 76 " --> pdb=" O LEU D 68 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 101 through 104 removed outlier: 3.516A pdb=" N ASP D 130 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 111 through 113 removed outlier: 6.839A pdb=" N ARG D 111 " --> pdb=" O LEU D 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.036A pdb=" N ARG D 321 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 151 through 152 Processing sheet with id=AD6, first strand: chain 'D' and resid 209 through 214 removed outlier: 6.419A pdb=" N SER D 209 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE D 277 " --> pdb=" O SER D 209 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL D 211 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N THR D 279 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA D 213 " --> pdb=" O THR D 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 359 through 360 removed outlier: 4.424A pdb=" N PHE D 359 " --> pdb=" O ASN D 374 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 48 through 51 removed outlier: 3.788A pdb=" N VAL E 49 " --> pdb=" O GLY E 58 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL E 60 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN E 71 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG E 62 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 68 " --> pdb=" O ALA E 37 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA E 37 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLU E 38 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE E 27 " --> pdb=" O GLU E 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 93 through 95 Processing sheet with id=AE1, first strand: chain 'E' and resid 104 through 105 Processing sheet with id=AE2, first strand: chain 'E' and resid 159 through 161 Processing sheet with id=AE3, first strand: chain 'E' and resid 151 through 152 removed outlier: 6.955A pdb=" N GLU E 199 " --> pdb=" O THR E 183 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 225 through 226 removed outlier: 4.023A pdb=" N GLU E 225 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 301 through 302 removed outlier: 3.541A pdb=" N GLU E 309 " --> pdb=" O THR E 302 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 34 through 35 removed outlier: 3.632A pdb=" N ARG F 74 " --> pdb=" O ARG F 71 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU F 69 " --> pdb=" O ILE F 76 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLN F 78 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL F 67 " --> pdb=" O GLN F 78 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 101 through 104 removed outlier: 3.721A pdb=" N ASP F 130 " --> pdb=" O VAL F 104 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 112 through 113 removed outlier: 7.513A pdb=" N ALA F 213 " --> pdb=" O THR F 279 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 144 through 145 removed outlier: 3.791A pdb=" N ARG F 321 " --> pdb=" O ILE F 145 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 150 through 151 removed outlier: 4.616A pdb=" N ILE F 164 " --> pdb=" O ILE F 151 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 208 through 210 removed outlier: 6.202A pdb=" N SER F 209 " --> pdb=" O LEU F 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'K' and resid 171 through 174 removed outlier: 3.507A pdb=" N VAL K 189 " --> pdb=" O LYS K 140 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL K 188 " --> pdb=" O ASN K 201 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 95 through 96 removed outlier: 4.093A pdb=" N ARG M 95 " --> pdb=" O GLU M 110 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 99 through 100 Processing sheet with id=AF6, first strand: chain 'N' and resid 38 through 39 removed outlier: 7.524A pdb=" N PHE N 38 " --> pdb=" O ILE N 8 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL N 10 " --> pdb=" O PHE N 38 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU N 7 " --> pdb=" O ALA N 65 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU N 67 " --> pdb=" O LEU N 7 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA N 9 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE N 69 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE N 11 " --> pdb=" O ILE N 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU N 92 " --> pdb=" O LEU N 67 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 28 through 29 Processing sheet with id=AF8, first strand: chain 'P' and resid 99 through 103 removed outlier: 5.813A pdb=" N LEU P 100 " --> pdb=" O ARG P 271 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG P 271 " --> pdb=" O LEU P 100 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR P 102 " --> pdb=" O VAL P 269 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA P 266 " --> pdb=" O LYS P 135 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE P 165 " --> pdb=" O TYR P 145 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU P 166 " --> pdb=" O TYR P 205 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 241 through 243 1992 hydrogen bonds defined for protein. 5751 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.42 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13118 1.34 - 1.46: 5997 1.46 - 1.58: 20907 1.58 - 1.69: 0 1.69 - 1.81: 225 Bond restraints: 40247 Sorted by residual: bond pdb=" CG MET A 547 " pdb=" SD MET A 547 " ideal model delta sigma weight residual 1.803 1.760 0.043 2.50e-02 1.60e+03 2.91e+00 bond pdb=" CG GLU G 46 " pdb=" CD GLU G 46 " ideal model delta sigma weight residual 1.516 1.485 0.031 2.50e-02 1.60e+03 1.59e+00 bond pdb=" CA VAL B 34 " pdb=" CB VAL B 34 " ideal model delta sigma weight residual 1.550 1.539 0.012 1.03e-02 9.43e+03 1.30e+00 bond pdb=" C ILE D 467 " pdb=" N TYR D 468 " ideal model delta sigma weight residual 1.331 1.299 0.032 2.83e-02 1.25e+03 1.29e+00 bond pdb=" CG LYS O 165 " pdb=" CD LYS O 165 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.22e+00 ... (remaining 40242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 53391 1.52 - 3.05: 745 3.05 - 4.57: 210 4.57 - 6.10: 23 6.10 - 7.62: 4 Bond angle restraints: 54373 Sorted by residual: angle pdb=" N GLU B 206 " pdb=" CA GLU B 206 " pdb=" CB GLU B 206 " ideal model delta sigma weight residual 114.17 109.95 4.22 1.14e+00 7.69e-01 1.37e+01 angle pdb=" C ILE G 45 " pdb=" N GLU G 46 " pdb=" CA GLU G 46 " ideal model delta sigma weight residual 120.68 114.64 6.04 1.70e+00 3.46e-01 1.26e+01 angle pdb=" N VAL F 375 " pdb=" CA VAL F 375 " pdb=" C VAL F 375 " ideal model delta sigma weight residual 113.71 110.57 3.14 9.50e-01 1.11e+00 1.09e+01 angle pdb=" C MET A 546 " pdb=" N MET A 547 " pdb=" CA MET A 547 " ideal model delta sigma weight residual 120.31 115.37 4.94 1.52e+00 4.33e-01 1.05e+01 angle pdb=" N GLU G 46 " pdb=" CA GLU G 46 " pdb=" CB GLU G 46 " ideal model delta sigma weight residual 110.30 115.04 -4.74 1.54e+00 4.22e-01 9.47e+00 ... (remaining 54368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 22602 17.81 - 35.62: 1777 35.62 - 53.43: 236 53.43 - 71.24: 36 71.24 - 89.05: 13 Dihedral angle restraints: 24664 sinusoidal: 10040 harmonic: 14624 Sorted by residual: dihedral pdb=" CA VAL F 291 " pdb=" C VAL F 291 " pdb=" N SER F 292 " pdb=" CA SER F 292 " ideal model delta harmonic sigma weight residual 180.00 150.38 29.62 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA HIS E 450 " pdb=" C HIS E 450 " pdb=" N PHE E 451 " pdb=" CA PHE E 451 " ideal model delta harmonic sigma weight residual -180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ALA P 214 " pdb=" C ALA P 214 " pdb=" N ILE P 215 " pdb=" CA ILE P 215 " ideal model delta harmonic sigma weight residual 180.00 157.55 22.45 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 24661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 4089 0.031 - 0.061: 1344 0.061 - 0.092: 384 0.092 - 0.122: 284 0.122 - 0.153: 35 Chirality restraints: 6136 Sorted by residual: chirality pdb=" CA MET A 485 " pdb=" N MET A 485 " pdb=" C MET A 485 " pdb=" CB MET A 485 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CA ILE N 11 " pdb=" N ILE N 11 " pdb=" C ILE N 11 " pdb=" CB ILE N 11 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA ILE N 28 " pdb=" N ILE N 28 " pdb=" C ILE N 28 " pdb=" CB ILE N 28 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 6133 not shown) Planarity restraints: 7056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA P 119 " 0.064 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO P 120 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO P 120 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO P 120 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 468 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO F 469 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO F 469 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 469 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 87 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C LYS I 87 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS I 87 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL I 88 " -0.012 2.00e-02 2.50e+03 ... (remaining 7053 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 421 2.49 - 3.09: 32480 3.09 - 3.69: 60318 3.69 - 4.30: 84711 4.30 - 4.90: 139796 Nonbonded interactions: 317726 Sorted by model distance: nonbonded pdb=" OG1 THR N 58 " pdb=" OE1 GLU N 59 " model vdw 1.886 3.040 nonbonded pdb=" O ARG I 85 " pdb=" OG SER I 90 " model vdw 1.900 3.040 nonbonded pdb=" OD1 ASP N 13 " pdb=" OG1 THR N 16 " model vdw 1.928 3.040 nonbonded pdb=" OG SER C 93 " pdb=" OG1 THR C 214 " model vdw 1.955 3.040 nonbonded pdb=" O LEU D 266 " pdb=" OG1 THR D 270 " model vdw 1.972 3.040 ... (remaining 317721 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 9 through 195 or resid 207 through 487)) selection = chain 'D' selection = (chain 'F' and (resid 9 through 195 or resid 207 through 487)) } ncs_group { reference = (chain 'G' and resid 31 through 232) selection = (chain 'I' and resid 31 through 232) selection = (chain 'K' and (resid 31 through 231 or (resid 232 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'H' selection = chain 'J' } 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: 6.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 34.760 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.002 0.043 40247 Z= 0.122 Angle : 0.516 7.622 54373 Z= 0.286 Chirality : 0.039 0.153 6136 Planarity : 0.003 0.097 7056 Dihedral : 12.573 89.053 15248 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.13), residues: 5003 helix: 1.66 (0.11), residues: 2205 sheet: -2.15 (0.23), residues: 542 loop : -1.59 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 5 TYR 0.018 0.001 TYR K 43 PHE 0.013 0.001 PHE E 258 TRP 0.021 0.001 TRP O 303 HIS 0.008 0.001 HIS P 241 Details of bonding type rmsd covalent geometry : bond 0.00247 (40247) covalent geometry : angle 0.51598 (54373) hydrogen bonds : bond 0.15667 ( 1992) hydrogen bonds : angle 6.20951 ( 5751) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 488 time to evaluate : 1.343 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: O 29 LYS cc_start: 0.4576 (tppt) cc_final: 0.4173 (mmtt) REVERT: O 53 PHE cc_start: 0.5899 (m-80) cc_final: 0.4835 (m-80) REVERT: O 116 TRP cc_start: 0.6879 (t-100) cc_final: 0.6000 (t-100) REVERT: O 130 LEU cc_start: 0.8516 (mt) cc_final: 0.8309 (mt) REVERT: O 152 TYR cc_start: 0.8490 (t80) cc_final: 0.7828 (t80) REVERT: O 251 ARG cc_start: 0.6358 (mmt90) cc_final: 0.6045 (tpp-160) REVERT: O 327 ILE cc_start: 0.4876 (mp) cc_final: 0.4660 (mt) REVERT: O 339 LYS cc_start: 0.5375 (tmmt) cc_final: 0.4728 (ptmt) REVERT: O 388 TYR cc_start: 0.5216 (m-80) cc_final: 0.4121 (m-80) REVERT: G 11 ASN cc_start: 0.6924 (p0) cc_final: 0.6616 (t0) REVERT: G 15 ASP cc_start: 0.6610 (m-30) cc_final: 0.6408 (m-30) REVERT: G 20 MET cc_start: 0.5159 (mtp) cc_final: 0.4525 (mtt) REVERT: G 23 PHE cc_start: 0.3114 (p90) cc_final: 0.2873 (p90) REVERT: G 43 TYR cc_start: 0.8078 (t80) cc_final: 0.7656 (t80) REVERT: G 152 MET cc_start: 0.6623 (ptt) cc_final: 0.6422 (ptt) REVERT: G 181 LYS cc_start: 0.4694 (mmtm) cc_final: 0.4394 (mmtm) REVERT: H 23 LYS cc_start: 0.8545 (tmmt) cc_final: 0.8252 (tptt) REVERT: H 57 PHE cc_start: 0.8390 (t80) cc_final: 0.7520 (t80) REVERT: B 317 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8165 (tp30) REVERT: B 383 MET cc_start: 0.9396 (ttm) cc_final: 0.9002 (ttm) REVERT: C 324 MET cc_start: 0.8754 (mmp) cc_final: 0.7952 (mpp) REVERT: D 150 MET cc_start: 0.8649 (tmm) cc_final: 0.8077 (tmm) REVERT: D 161 MET cc_start: 0.9053 (mpp) cc_final: 0.8720 (mpp) REVERT: D 383 MET cc_start: 0.8731 (ttp) cc_final: 0.8380 (ttp) REVERT: E 295 MET cc_start: 0.8156 (ppp) cc_final: 0.7934 (ppp) REVERT: E 352 MET cc_start: 0.8961 (tmm) cc_final: 0.8404 (tmm) REVERT: E 374 MET cc_start: 0.9104 (tpp) cc_final: 0.7969 (tpp) REVERT: E 546 MET cc_start: 0.9269 (ttp) cc_final: 0.8941 (ttm) REVERT: E 611 PHE cc_start: 0.7786 (m-80) cc_final: 0.7129 (m-80) REVERT: F 207 ASN cc_start: 0.7516 (m-40) cc_final: 0.7258 (t0) REVERT: F 280 ASP cc_start: 0.8559 (t0) cc_final: 0.8265 (m-30) REVERT: K 70 MET cc_start: 0.8461 (tmm) cc_final: 0.8242 (ttp) REVERT: L 61 ASN cc_start: 0.7506 (p0) cc_final: 0.6971 (p0) REVERT: M 118 ASN cc_start: 0.6048 (p0) cc_final: 0.5643 (m-40) REVERT: M 139 TYR cc_start: 0.7333 (t80) cc_final: 0.7117 (t80) REVERT: N 53 LYS cc_start: 0.7970 (mmmt) cc_final: 0.7471 (ptmm) REVERT: J 18 HIS cc_start: 0.8665 (m90) cc_final: 0.8305 (m170) REVERT: J 26 LYS cc_start: 0.8902 (mppt) cc_final: 0.8570 (pttp) REVERT: P 91 ARG cc_start: 0.8272 (tpt170) cc_final: 0.7903 (tpm170) REVERT: P 96 THR cc_start: 0.3301 (m) cc_final: 0.2784 (m) REVERT: P 105 GLU cc_start: 0.8313 (tp30) cc_final: 0.8010 (tp30) REVERT: P 112 HIS cc_start: 0.8664 (t-170) cc_final: 0.8285 (t-90) REVERT: P 260 LYS cc_start: 0.8612 (mmmt) cc_final: 0.8288 (mmmm) outliers start: 0 outliers final: 0 residues processed: 488 average time/residue: 0.2466 time to fit residues: 189.6319 Evaluate side-chains 252 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.0060 chunk 494 optimal weight: 20.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 overall best weight: 4.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 18 GLN O 35 ASN O 87 GLN O 136 ASN O 153 ASN ** O 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 282 GLN ** O 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 HIS B 66 GLN C 248 GLN C 349 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 GLN F 396 HIS ** N 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 94 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.068596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047052 restraints weight = 224004.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.047930 restraints weight = 121642.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.048669 restraints weight = 81965.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048994 restraints weight = 65031.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.049223 restraints weight = 57125.246| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 40247 Z= 0.250 Angle : 0.703 10.192 54373 Z= 0.371 Chirality : 0.047 0.281 6136 Planarity : 0.005 0.072 7056 Dihedral : 4.785 36.237 5459 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.88 % Allowed : 7.50 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % 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: -0.38 (0.12), residues: 5003 helix: 1.34 (0.11), residues: 2234 sheet: -2.10 (0.22), residues: 558 loop : -1.43 (0.14), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 156 TYR 0.042 0.002 TYR I 43 PHE 0.042 0.002 PHE K 62 TRP 0.028 0.002 TRP E 567 HIS 0.008 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00553 (40247) covalent geometry : angle 0.70260 (54373) hydrogen bonds : bond 0.05089 ( 1992) hydrogen bonds : angle 5.18011 ( 5751) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 264 time to evaluate : 1.218 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: G 11 ASN cc_start: 0.6652 (p0) cc_final: 0.6407 (t0) REVERT: G 15 ASP cc_start: 0.6701 (m-30) cc_final: 0.6444 (m-30) REVERT: G 152 MET cc_start: 0.6466 (ptt) cc_final: 0.6191 (ptt) REVERT: G 181 LYS cc_start: 0.5142 (mmtm) cc_final: 0.4862 (mmtm) REVERT: H 23 LYS cc_start: 0.8625 (tmmt) cc_final: 0.8365 (tptt) REVERT: H 49 GLN cc_start: 0.8893 (mm110) cc_final: 0.8160 (tm-30) REVERT: C 45 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8264 (tpp) REVERT: C 324 MET cc_start: 0.8262 (mmp) cc_final: 0.7981 (mpp) REVERT: C 607 MET cc_start: 0.9253 (ptm) cc_final: 0.8657 (ppp) REVERT: D 150 MET cc_start: 0.8805 (tmm) cc_final: 0.8262 (tmm) REVERT: D 383 MET cc_start: 0.8850 (ttp) cc_final: 0.8627 (ttp) REVERT: E 607 MET cc_start: 0.8618 (ptm) cc_final: 0.8170 (ppp) REVERT: F 416 MET cc_start: 0.9024 (tmm) cc_final: 0.8620 (tmm) REVERT: N 47 LYS cc_start: 0.6992 (tmtt) cc_final: 0.6589 (mmmt) REVERT: N 53 LYS cc_start: 0.7522 (mmmt) cc_final: 0.7116 (mttm) REVERT: I 21 GLN cc_start: 0.8578 (tp-100) cc_final: 0.8236 (pt0) REVERT: J 18 HIS cc_start: 0.8751 (m90) cc_final: 0.8499 (m170) REVERT: P 72 LYS cc_start: 0.6533 (mmmt) cc_final: 0.6264 (mmmt) REVERT: P 91 ARG cc_start: 0.8163 (tpt170) cc_final: 0.7550 (tpm170) REVERT: P 105 GLU cc_start: 0.8514 (tp30) cc_final: 0.8130 (tp30) REVERT: P 112 HIS cc_start: 0.8689 (t-170) cc_final: 0.8278 (t-90) REVERT: P 224 MET cc_start: 0.8712 (mmp) cc_final: 0.8507 (mmp) REVERT: P 260 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8350 (mmmm) outliers start: 38 outliers final: 18 residues processed: 290 average time/residue: 0.2287 time to fit residues: 108.3531 Evaluate side-chains 230 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain P residue 237 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 409 optimal weight: 9.9990 chunk 327 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 173 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 358 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 480 optimal weight: 5.9990 chunk 239 optimal weight: 0.9980 chunk 434 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 ASN ** O 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 324 HIS ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN H 18 HIS ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.067893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.047662 restraints weight = 224354.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.048839 restraints weight = 117215.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.049591 restraints weight = 76722.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.050021 restraints weight = 58236.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.050439 restraints weight = 49423.118| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 40247 Z= 0.224 Angle : 0.640 11.358 54373 Z= 0.338 Chirality : 0.044 0.232 6136 Planarity : 0.004 0.055 7056 Dihedral : 4.756 37.300 5459 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.39 % Allowed : 10.59 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % 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: -0.35 (0.12), residues: 5003 helix: 1.34 (0.11), residues: 2232 sheet: -1.95 (0.22), residues: 570 loop : -1.41 (0.14), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 610 TYR 0.040 0.001 TYR I 43 PHE 0.030 0.002 PHE G 23 TRP 0.015 0.001 TRP O 303 HIS 0.007 0.001 HIS B 344 Details of bonding type rmsd covalent geometry : bond 0.00495 (40247) covalent geometry : angle 0.64026 (54373) hydrogen bonds : bond 0.04846 ( 1992) hydrogen bonds : angle 4.97692 ( 5751) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 223 time to evaluate : 1.458 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: G 11 ASN cc_start: 0.6855 (p0) cc_final: 0.6609 (t0) REVERT: H 23 LYS cc_start: 0.8446 (tmmt) cc_final: 0.8028 (tptt) REVERT: H 25 ARG cc_start: 0.8634 (ptt-90) cc_final: 0.8390 (ptt-90) REVERT: H 49 GLN cc_start: 0.8883 (mm110) cc_final: 0.8105 (tm-30) REVERT: B 337 MET cc_start: 0.9278 (mtm) cc_final: 0.9009 (mtp) REVERT: C 45 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8354 (tpp) REVERT: C 324 MET cc_start: 0.8384 (mmp) cc_final: 0.8018 (mpp) REVERT: C 374 MET cc_start: 0.8673 (tpp) cc_final: 0.8467 (tpp) REVERT: C 547 MET cc_start: 0.8967 (ppp) cc_final: 0.8627 (ppp) REVERT: C 604 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.8930 (tt) REVERT: C 607 MET cc_start: 0.9257 (ptm) cc_final: 0.8709 (ppp) REVERT: D 150 MET cc_start: 0.8795 (tmm) cc_final: 0.8017 (tmm) REVERT: D 383 MET cc_start: 0.8882 (ttp) cc_final: 0.8563 (ttp) REVERT: E 324 MET cc_start: 0.9212 (mtt) cc_final: 0.8955 (mtt) REVERT: E 547 MET cc_start: 0.9037 (ptm) cc_final: 0.8611 (ptp) REVERT: E 607 MET cc_start: 0.8675 (ptm) cc_final: 0.8228 (ppp) REVERT: K 157 MET cc_start: 0.8812 (mmm) cc_final: 0.8579 (mmm) REVERT: M 18 MET cc_start: 0.8884 (mmp) cc_final: 0.8666 (mmp) REVERT: N 47 LYS cc_start: 0.6895 (tmtt) cc_final: 0.6417 (mmmt) REVERT: I 157 MET cc_start: 0.8750 (mmt) cc_final: 0.8527 (mmt) REVERT: J 18 HIS cc_start: 0.8745 (m90) cc_final: 0.8015 (m170) REVERT: P 91 ARG cc_start: 0.8477 (tpt170) cc_final: 0.7790 (tpm170) REVERT: P 112 HIS cc_start: 0.8540 (t-170) cc_final: 0.8245 (t-90) REVERT: P 156 ARG cc_start: 0.7842 (ptp-170) cc_final: 0.7528 (ptp-170) REVERT: P 224 MET cc_start: 0.8882 (mmp) cc_final: 0.8505 (mmp) outliers start: 60 outliers final: 35 residues processed: 268 average time/residue: 0.2096 time to fit residues: 94.6917 Evaluate side-chains 232 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 34 PHE Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain G residue 20 MET Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain J residue 77 GLN Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain P residue 73 ASN Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 236 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 121 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 354 optimal weight: 10.0000 chunk 112 optimal weight: 5.9990 chunk 286 optimal weight: 6.9990 chunk 264 optimal weight: 6.9990 chunk 408 optimal weight: 10.0000 chunk 284 optimal weight: 9.9990 chunk 472 optimal weight: 5.9990 chunk 384 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN C 237 GLN C 288 ASN D 12 ASN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 GLN ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 GLN ** N 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.066575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.045344 restraints weight = 222587.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.046299 restraints weight = 120017.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.046843 restraints weight = 81369.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047249 restraints weight = 64189.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.047462 restraints weight = 55507.166| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 40247 Z= 0.318 Angle : 0.715 10.919 54373 Z= 0.376 Chirality : 0.046 0.187 6136 Planarity : 0.005 0.051 7056 Dihedral : 5.038 38.008 5459 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.14 % Allowed : 12.70 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.12), residues: 5003 helix: 1.13 (0.11), residues: 2229 sheet: -2.00 (0.21), residues: 588 loop : -1.54 (0.14), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 156 TYR 0.038 0.002 TYR I 43 PHE 0.029 0.002 PHE E 258 TRP 0.013 0.002 TRP O 303 HIS 0.010 0.002 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00704 (40247) covalent geometry : angle 0.71529 (54373) hydrogen bonds : bond 0.05117 ( 1992) hydrogen bonds : angle 5.09419 ( 5751) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 199 time to evaluate : 1.418 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: G 11 ASN cc_start: 0.6621 (p0) cc_final: 0.6402 (t0) REVERT: H 23 LYS cc_start: 0.8597 (tmmt) cc_final: 0.8220 (tptt) REVERT: A 297 PHE cc_start: 0.9412 (OUTLIER) cc_final: 0.8567 (t80) REVERT: A 312 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7855 (mpp) REVERT: A 352 MET cc_start: 0.8366 (ttt) cc_final: 0.8087 (ttt) REVERT: A 546 MET cc_start: 0.9369 (mtp) cc_final: 0.9101 (mtp) REVERT: B 337 MET cc_start: 0.9340 (mtm) cc_final: 0.9106 (mtp) REVERT: C 45 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8381 (tpp) REVERT: C 101 MET cc_start: 0.9037 (tpp) cc_final: 0.8821 (tpp) REVERT: C 312 MET cc_start: 0.9298 (mmm) cc_final: 0.8385 (tpp) REVERT: C 324 MET cc_start: 0.8621 (mmp) cc_final: 0.8168 (mpp) REVERT: C 547 MET cc_start: 0.8972 (ppp) cc_final: 0.8620 (ppp) REVERT: C 604 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.8970 (tt) REVERT: C 607 MET cc_start: 0.9301 (ptm) cc_final: 0.8704 (ppp) REVERT: D 150 MET cc_start: 0.8813 (tmm) cc_final: 0.8032 (tmm) REVERT: D 383 MET cc_start: 0.8978 (ttp) cc_final: 0.8657 (ttp) REVERT: E 324 MET cc_start: 0.9283 (mtt) cc_final: 0.8807 (mtt) REVERT: E 482 ARG cc_start: 0.9362 (OUTLIER) cc_final: 0.8971 (ptp90) REVERT: E 607 MET cc_start: 0.8770 (ptm) cc_final: 0.8297 (ppp) REVERT: M 118 ASN cc_start: 0.6321 (p0) cc_final: 0.5674 (m-40) REVERT: M 221 MET cc_start: 0.8565 (tpp) cc_final: 0.8054 (tmm) REVERT: N 47 LYS cc_start: 0.6888 (tmtt) cc_final: 0.6423 (mmmt) REVERT: I 157 MET cc_start: 0.8650 (mmt) cc_final: 0.8156 (mmt) REVERT: J 18 HIS cc_start: 0.8598 (m90) cc_final: 0.8267 (m170) REVERT: J 26 LYS cc_start: 0.8973 (mppt) cc_final: 0.8755 (pttm) REVERT: J 61 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7248 (p0) REVERT: P 91 ARG cc_start: 0.8367 (tpt170) cc_final: 0.7659 (tpm170) REVERT: P 112 HIS cc_start: 0.8742 (t-170) cc_final: 0.8323 (t-90) outliers start: 92 outliers final: 54 residues processed: 275 average time/residue: 0.2093 time to fit residues: 97.9320 Evaluate side-chains 246 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 186 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 34 PHE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 210 TYR Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain F residue 472 MET Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 178 TYR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 168 LYS Chi-restraints excluded: chain P residue 236 ASP Chi-restraints excluded: chain P residue 237 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 111 optimal weight: 3.9990 chunk 324 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 78 optimal weight: 0.7980 chunk 289 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 453 optimal weight: 9.9990 chunk 384 optimal weight: 5.9990 chunk 230 optimal weight: 0.0970 chunk 309 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 136 ASN ** O 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 GLN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 GLN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 GLN N 70 ASN N 72 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.067778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.047717 restraints weight = 221904.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.048904 restraints weight = 115488.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.049694 restraints weight = 75358.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.050211 restraints weight = 57112.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.050501 restraints weight = 47947.349| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40247 Z= 0.138 Angle : 0.592 11.299 54373 Z= 0.311 Chirality : 0.043 0.237 6136 Planarity : 0.004 0.044 7056 Dihedral : 4.711 37.025 5459 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.88 % Allowed : 13.98 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % 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: -0.31 (0.12), residues: 5003 helix: 1.35 (0.11), residues: 2239 sheet: -1.83 (0.22), residues: 559 loop : -1.40 (0.14), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 223 TYR 0.030 0.001 TYR I 43 PHE 0.037 0.001 PHE C 258 TRP 0.011 0.001 TRP C 567 HIS 0.014 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00298 (40247) covalent geometry : angle 0.59223 (54373) hydrogen bonds : bond 0.04454 ( 1992) hydrogen bonds : angle 4.78982 ( 5751) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 209 time to evaluate : 1.478 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: O 105 MET cc_start: 0.7112 (mmt) cc_final: 0.6447 (ppp) REVERT: G 44 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8375 (pm20) REVERT: H 23 LYS cc_start: 0.8513 (tmmt) cc_final: 0.8085 (tptt) REVERT: A 297 PHE cc_start: 0.9377 (OUTLIER) cc_final: 0.8754 (t80) REVERT: A 352 MET cc_start: 0.8331 (ttt) cc_final: 0.8056 (ttt) REVERT: C 324 MET cc_start: 0.8395 (mmp) cc_final: 0.8129 (mpp) REVERT: C 471 TYR cc_start: 0.9173 (OUTLIER) cc_final: 0.8772 (m-10) REVERT: C 547 MET cc_start: 0.9039 (ppp) cc_final: 0.8786 (ppp) REVERT: C 604 LEU cc_start: 0.9620 (OUTLIER) cc_final: 0.8956 (tt) REVERT: C 607 MET cc_start: 0.9244 (ptm) cc_final: 0.8692 (ppp) REVERT: D 150 MET cc_start: 0.8888 (tmm) cc_final: 0.8164 (tmm) REVERT: D 151 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.8797 (mp) REVERT: D 383 MET cc_start: 0.8892 (ttp) cc_final: 0.8537 (ttp) REVERT: E 324 MET cc_start: 0.9254 (mtt) cc_final: 0.8789 (mtt) REVERT: E 348 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8987 (mtpp) REVERT: E 482 ARG cc_start: 0.9304 (OUTLIER) cc_final: 0.8932 (ptp90) REVERT: E 607 MET cc_start: 0.8816 (ptm) cc_final: 0.8403 (ppp) REVERT: M 118 ASN cc_start: 0.6496 (p0) cc_final: 0.5752 (m-40) REVERT: N 47 LYS cc_start: 0.6788 (tmtt) cc_final: 0.6368 (mmmt) REVERT: I 82 ASN cc_start: 0.9108 (t0) cc_final: 0.8388 (p0) REVERT: I 157 MET cc_start: 0.8571 (mmt) cc_final: 0.7983 (mmt) REVERT: J 18 HIS cc_start: 0.8546 (m90) cc_final: 0.8147 (m170) REVERT: J 53 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7557 (pp20) REVERT: P 72 LYS cc_start: 0.6640 (mmmt) cc_final: 0.6326 (mmtm) REVERT: P 91 ARG cc_start: 0.8577 (tpt170) cc_final: 0.7906 (tpm170) REVERT: P 93 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: P 112 HIS cc_start: 0.8550 (t-170) cc_final: 0.8273 (t-90) outliers start: 81 outliers final: 46 residues processed: 275 average time/residue: 0.2102 time to fit residues: 97.6765 Evaluate side-chains 244 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 210 TYR Chi-restraints excluded: chain G residue 44 GLU Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 348 LYS Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 178 TYR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 236 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 327 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 309 optimal weight: 0.0270 chunk 210 optimal weight: 6.9990 chunk 408 optimal weight: 5.9990 chunk 339 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 242 ASN ** O 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** 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 = 0.3489 r_free = 0.3489 target = 0.067366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.045982 restraints weight = 221363.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.046979 restraints weight = 119233.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.047549 restraints weight = 80424.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.047963 restraints weight = 63326.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.048259 restraints weight = 54709.747| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 40247 Z= 0.203 Angle : 0.621 12.660 54373 Z= 0.326 Chirality : 0.044 0.269 6136 Planarity : 0.004 0.047 7056 Dihedral : 4.705 37.202 5459 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.21 % Allowed : 14.53 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % 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: -0.32 (0.12), residues: 5003 helix: 1.35 (0.11), residues: 2234 sheet: -1.92 (0.21), residues: 578 loop : -1.38 (0.14), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 482 TYR 0.032 0.001 TYR I 43 PHE 0.027 0.002 PHE C 423 TRP 0.010 0.001 TRP C 567 HIS 0.017 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00453 (40247) covalent geometry : angle 0.62116 (54373) hydrogen bonds : bond 0.04476 ( 1992) hydrogen bonds : angle 4.81479 ( 5751) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 198 time to evaluate : 1.630 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: O 105 MET cc_start: 0.5898 (mmt) cc_final: 0.5532 (ppp) REVERT: G 43 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6987 (m-80) REVERT: H 23 LYS cc_start: 0.8647 (tmmt) cc_final: 0.8303 (tptt) REVERT: H 34 GLN cc_start: 0.8637 (mm-40) cc_final: 0.8436 (tm-30) REVERT: A 297 PHE cc_start: 0.9390 (OUTLIER) cc_final: 0.8711 (t80) REVERT: A 312 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7973 (mpp) REVERT: A 352 MET cc_start: 0.8402 (ttt) cc_final: 0.8155 (ttt) REVERT: A 607 MET cc_start: 0.9096 (ptt) cc_final: 0.8767 (ppp) REVERT: B 289 ARG cc_start: 0.9456 (OUTLIER) cc_final: 0.9175 (ptp-110) REVERT: B 383 MET cc_start: 0.8998 (ttm) cc_final: 0.8575 (tpp) REVERT: C 312 MET cc_start: 0.9283 (mmm) cc_final: 0.8381 (tpp) REVERT: C 324 MET cc_start: 0.8500 (mmp) cc_final: 0.8063 (mpp) REVERT: C 471 TYR cc_start: 0.9192 (OUTLIER) cc_final: 0.8802 (m-10) REVERT: C 547 MET cc_start: 0.9004 (ppp) cc_final: 0.8757 (ppp) REVERT: C 604 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.8940 (tt) REVERT: C 607 MET cc_start: 0.9300 (ptm) cc_final: 0.8716 (ppp) REVERT: D 150 MET cc_start: 0.8932 (tmm) cc_final: 0.8226 (tmm) REVERT: D 151 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8866 (mp) REVERT: D 383 MET cc_start: 0.9027 (ttp) cc_final: 0.8650 (ttp) REVERT: E 324 MET cc_start: 0.9336 (mtt) cc_final: 0.8631 (mpp) REVERT: E 348 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8983 (mtpp) REVERT: E 482 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.8845 (ptp90) REVERT: M 118 ASN cc_start: 0.6469 (p0) cc_final: 0.5830 (m-40) REVERT: N 47 LYS cc_start: 0.7022 (tmtt) cc_final: 0.6556 (mmmt) REVERT: I 82 ASN cc_start: 0.9121 (t0) cc_final: 0.8397 (p0) REVERT: J 18 HIS cc_start: 0.8517 (m90) cc_final: 0.8180 (m170) REVERT: J 53 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7484 (pp20) REVERT: P 72 LYS cc_start: 0.6416 (mmmt) cc_final: 0.6010 (mmtt) REVERT: P 91 ARG cc_start: 0.8331 (tpt170) cc_final: 0.7633 (tpm170) outliers start: 95 outliers final: 59 residues processed: 277 average time/residue: 0.2139 time to fit residues: 101.0332 Evaluate side-chains 251 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 182 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 210 TYR Chi-restraints excluded: chain G residue 43 TYR Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 348 LYS Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 178 TYR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 236 ASP Chi-restraints excluded: chain P residue 237 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 176 optimal weight: 0.8980 chunk 164 optimal weight: 7.9990 chunk 321 optimal weight: 0.0070 chunk 52 optimal weight: 5.9990 chunk 333 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 272 optimal weight: 8.9990 chunk 365 optimal weight: 5.9990 chunk 320 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 366 optimal weight: 0.7980 overall best weight: 2.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.067700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.046524 restraints weight = 219751.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.047529 restraints weight = 118482.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.048117 restraints weight = 78663.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.048479 restraints weight = 61652.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.048667 restraints weight = 53236.784| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 40247 Z= 0.161 Angle : 0.600 16.243 54373 Z= 0.312 Chirality : 0.043 0.233 6136 Planarity : 0.004 0.048 7056 Dihedral : 4.608 37.001 5459 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.23 % Allowed : 14.93 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % 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: -0.24 (0.12), residues: 5003 helix: 1.39 (0.11), residues: 2239 sheet: -1.81 (0.21), residues: 581 loop : -1.33 (0.14), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 85 TYR 0.029 0.001 TYR I 43 PHE 0.051 0.001 PHE K 62 TRP 0.013 0.001 TRP O 303 HIS 0.018 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00356 (40247) covalent geometry : angle 0.59969 (54373) hydrogen bonds : bond 0.04280 ( 1992) hydrogen bonds : angle 4.70466 ( 5751) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 190 time to evaluate : 1.437 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: O 105 MET cc_start: 0.5902 (mmt) cc_final: 0.5516 (tmm) REVERT: G 43 TYR cc_start: 0.7295 (OUTLIER) cc_final: 0.6859 (m-80) REVERT: H 23 LYS cc_start: 0.8590 (tmmt) cc_final: 0.8219 (tptt) REVERT: A 45 MET cc_start: 0.8584 (tpp) cc_final: 0.8367 (tpp) REVERT: A 297 PHE cc_start: 0.9355 (OUTLIER) cc_final: 0.8754 (t80) REVERT: A 352 MET cc_start: 0.8366 (ttt) cc_final: 0.8088 (ttm) REVERT: A 607 MET cc_start: 0.9127 (ptt) cc_final: 0.8825 (ppp) REVERT: B 289 ARG cc_start: 0.9432 (OUTLIER) cc_final: 0.9169 (ptp-110) REVERT: B 383 MET cc_start: 0.9019 (ttm) cc_final: 0.8645 (tpp) REVERT: C 324 MET cc_start: 0.8536 (mmp) cc_final: 0.8143 (mpp) REVERT: C 471 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.8747 (m-10) REVERT: C 604 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.8970 (tt) REVERT: C 607 MET cc_start: 0.9284 (ptm) cc_final: 0.8697 (ppp) REVERT: D 150 MET cc_start: 0.8973 (tmm) cc_final: 0.8288 (tmm) REVERT: D 151 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.8868 (mp) REVERT: D 383 MET cc_start: 0.8997 (ttp) cc_final: 0.8616 (ttp) REVERT: E 324 MET cc_start: 0.9356 (mtt) cc_final: 0.8630 (mpp) REVERT: E 348 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8986 (mtpp) REVERT: E 352 MET cc_start: 0.8356 (tmm) cc_final: 0.7906 (tmm) REVERT: E 482 ARG cc_start: 0.9314 (OUTLIER) cc_final: 0.8816 (ptp90) REVERT: F 215 MET cc_start: 0.9173 (pmm) cc_final: 0.8951 (pmm) REVERT: M 118 ASN cc_start: 0.6300 (p0) cc_final: 0.5809 (m-40) REVERT: N 47 LYS cc_start: 0.7022 (tmtt) cc_final: 0.6512 (mmmt) REVERT: I 82 ASN cc_start: 0.9090 (t0) cc_final: 0.8410 (p0) REVERT: I 157 MET cc_start: 0.8559 (mmt) cc_final: 0.7952 (mmt) REVERT: J 18 HIS cc_start: 0.8503 (m90) cc_final: 0.8142 (m170) REVERT: J 53 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7570 (pp20) REVERT: P 72 LYS cc_start: 0.6388 (mmmt) cc_final: 0.6003 (mmtt) REVERT: P 91 ARG cc_start: 0.8411 (tpt170) cc_final: 0.7658 (tpm170) outliers start: 96 outliers final: 65 residues processed: 274 average time/residue: 0.2147 time to fit residues: 100.4459 Evaluate side-chains 254 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 180 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 196 VAL Chi-restraints excluded: chain O residue 210 TYR Chi-restraints excluded: chain G residue 43 TYR Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 412 ILE Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 471 TYR Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 521 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 348 LYS Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain M residue 212 ASN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 236 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 255 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 317 optimal weight: 1.9990 chunk 347 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 155 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 407 optimal weight: 5.9990 chunk 315 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 274 HIS G 41 GLN ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 HIS ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 181 ASN ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.068684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.047446 restraints weight = 218066.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.048423 restraints weight = 115546.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049125 restraints weight = 77237.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.049449 restraints weight = 60316.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.049697 restraints weight = 52656.064| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 40247 Z= 0.110 Angle : 0.589 15.121 54373 Z= 0.301 Chirality : 0.042 0.223 6136 Planarity : 0.004 0.046 7056 Dihedral : 4.413 36.559 5459 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.69 % Allowed : 15.49 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % 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: -0.10 (0.12), residues: 5003 helix: 1.46 (0.11), residues: 2242 sheet: -1.68 (0.21), residues: 576 loop : -1.22 (0.14), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 85 TYR 0.025 0.001 TYR I 43 PHE 0.025 0.001 PHE E 258 TRP 0.012 0.001 TRP A 567 HIS 0.016 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00232 (40247) covalent geometry : angle 0.58851 (54373) hydrogen bonds : bond 0.03911 ( 1992) hydrogen bonds : angle 4.55536 ( 5751) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 210 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 119 ARG cc_start: 0.7307 (mmm-85) cc_final: 0.6920 (ttt180) REVERT: H 23 LYS cc_start: 0.8576 (tmmt) cc_final: 0.8125 (tptt) REVERT: H 61 ASN cc_start: 0.7945 (p0) cc_final: 0.7668 (m-40) REVERT: A 297 PHE cc_start: 0.9313 (OUTLIER) cc_final: 0.8696 (t80) REVERT: A 607 MET cc_start: 0.9121 (ptt) cc_final: 0.8804 (ppp) REVERT: B 289 ARG cc_start: 0.9374 (OUTLIER) cc_final: 0.9122 (ptp-110) REVERT: B 472 MET cc_start: 0.8427 (mmm) cc_final: 0.7901 (tmm) REVERT: C 324 MET cc_start: 0.8437 (mmp) cc_final: 0.7980 (mpp) REVERT: C 607 MET cc_start: 0.9291 (ptm) cc_final: 0.8744 (ppp) REVERT: D 150 MET cc_start: 0.8945 (tmm) cc_final: 0.8235 (tmm) REVERT: D 151 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.8905 (mp) REVERT: D 383 MET cc_start: 0.8922 (ttp) cc_final: 0.8537 (ttp) REVERT: E 324 MET cc_start: 0.9382 (mtt) cc_final: 0.8693 (mpp) REVERT: E 348 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.9016 (mtpp) REVERT: E 482 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.8787 (ptp90) REVERT: F 215 MET cc_start: 0.9167 (pmm) cc_final: 0.8910 (pmm) REVERT: F 230 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8544 (tp30) REVERT: M 118 ASN cc_start: 0.6413 (p0) cc_final: 0.5906 (m-40) REVERT: N 47 LYS cc_start: 0.6960 (tmtt) cc_final: 0.6468 (mmmt) REVERT: I 82 ASN cc_start: 0.9025 (t0) cc_final: 0.8459 (p0) REVERT: J 18 HIS cc_start: 0.8505 (m90) cc_final: 0.8152 (m170) REVERT: J 53 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7610 (pp20) REVERT: P 72 LYS cc_start: 0.6293 (mmmt) cc_final: 0.6084 (mmtt) REVERT: P 91 ARG cc_start: 0.8447 (tpt170) cc_final: 0.7681 (tpm170) REVERT: P 236 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7715 (p0) outliers start: 73 outliers final: 47 residues processed: 272 average time/residue: 0.2128 time to fit residues: 97.3137 Evaluate side-chains 244 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 190 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 196 VAL Chi-restraints excluded: chain O residue 210 TYR Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 348 LYS Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain E residue 533 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 236 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 18 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 473 optimal weight: 9.9990 chunk 312 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 457 optimal weight: 0.7980 chunk 475 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 597 HIS ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 252 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.067493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.046253 restraints weight = 220286.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.047224 restraints weight = 120549.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.047877 restraints weight = 81700.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048182 restraints weight = 64686.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.048397 restraints weight = 56875.500| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 40247 Z= 0.190 Angle : 0.626 14.349 54373 Z= 0.324 Chirality : 0.043 0.211 6136 Planarity : 0.004 0.072 7056 Dihedral : 4.527 37.030 5459 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.63 % Allowed : 15.86 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % 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: -0.18 (0.12), residues: 5003 helix: 1.41 (0.11), residues: 2248 sheet: -1.56 (0.21), residues: 596 loop : -1.34 (0.14), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 25 TYR 0.027 0.001 TYR I 43 PHE 0.027 0.002 PHE E 258 TRP 0.056 0.001 TRP A 567 HIS 0.010 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00425 (40247) covalent geometry : angle 0.62619 (54373) hydrogen bonds : bond 0.04302 ( 1992) hydrogen bonds : angle 4.67084 ( 5751) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 197 time to evaluate : 1.569 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: O 119 ARG cc_start: 0.7154 (mmm-85) cc_final: 0.6829 (ttt180) REVERT: H 61 ASN cc_start: 0.7865 (p0) cc_final: 0.7550 (m-40) REVERT: A 297 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8734 (t80) REVERT: A 312 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8129 (mpp) REVERT: A 607 MET cc_start: 0.9192 (ptt) cc_final: 0.8908 (ppp) REVERT: B 108 MET cc_start: 0.7903 (mtt) cc_final: 0.7634 (mtt) REVERT: B 289 ARG cc_start: 0.9436 (OUTLIER) cc_final: 0.9157 (ptp-110) REVERT: B 383 MET cc_start: 0.9110 (tpp) cc_final: 0.8758 (tpp) REVERT: C 604 LEU cc_start: 0.9583 (OUTLIER) cc_final: 0.9015 (tt) REVERT: C 607 MET cc_start: 0.9321 (ptm) cc_final: 0.8732 (ppp) REVERT: D 150 MET cc_start: 0.8927 (tmm) cc_final: 0.8141 (tmm) REVERT: D 151 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.9015 (tp) REVERT: D 383 MET cc_start: 0.9026 (ttp) cc_final: 0.8607 (ttp) REVERT: E 312 MET cc_start: 0.9134 (mmm) cc_final: 0.8102 (tmm) REVERT: E 324 MET cc_start: 0.9371 (mtt) cc_final: 0.8772 (mtt) REVERT: E 352 MET cc_start: 0.8810 (tmm) cc_final: 0.8285 (tmm) REVERT: E 482 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.8789 (ptp90) REVERT: F 215 MET cc_start: 0.9187 (pmm) cc_final: 0.8937 (pmm) REVERT: F 230 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8629 (tp30) REVERT: M 118 ASN cc_start: 0.6453 (p0) cc_final: 0.6029 (m-40) REVERT: M 193 ASP cc_start: 0.8720 (t0) cc_final: 0.8342 (p0) REVERT: N 47 LYS cc_start: 0.7031 (tmtt) cc_final: 0.6560 (mmmt) REVERT: I 82 ASN cc_start: 0.9145 (t0) cc_final: 0.8573 (p0) REVERT: I 157 MET cc_start: 0.8501 (mmt) cc_final: 0.8166 (mmt) REVERT: J 18 HIS cc_start: 0.8527 (m90) cc_final: 0.8200 (m170) REVERT: P 91 ARG cc_start: 0.8380 (tpt170) cc_final: 0.7625 (tpm170) REVERT: P 224 MET cc_start: 0.8809 (mmp) cc_final: 0.8541 (mmp) REVERT: P 236 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7557 (p0) outliers start: 70 outliers final: 55 residues processed: 257 average time/residue: 0.2140 time to fit residues: 92.7985 Evaluate side-chains 250 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 188 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 210 TYR Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 444 ILE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain D residue 11 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 236 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 252 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 498 optimal weight: 4.9990 chunk 52 optimal weight: 0.0000 chunk 346 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 337 optimal weight: 5.9990 chunk 497 optimal weight: 7.9990 chunk 301 optimal weight: 3.9990 chunk 324 optimal weight: 0.0470 overall best weight: 2.6088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 73 ASN ** G 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** 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 = 0.3499 r_free = 0.3499 target = 0.067711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.046629 restraints weight = 218637.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.047512 restraints weight = 117875.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.048100 restraints weight = 78765.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.048485 restraints weight = 61716.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.048739 restraints weight = 53583.683| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 40247 Z= 0.163 Angle : 0.621 17.249 54373 Z= 0.321 Chirality : 0.043 0.224 6136 Planarity : 0.004 0.061 7056 Dihedral : 4.504 36.881 5459 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.65 % Allowed : 16.00 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % 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: -0.17 (0.12), residues: 5003 helix: 1.39 (0.11), residues: 2248 sheet: -1.65 (0.21), residues: 600 loop : -1.27 (0.14), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 25 TYR 0.027 0.001 TYR I 43 PHE 0.050 0.001 PHE K 62 TRP 0.045 0.001 TRP A 567 HIS 0.007 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00364 (40247) covalent geometry : angle 0.62095 (54373) hydrogen bonds : bond 0.04161 ( 1992) hydrogen bonds : angle 4.63482 ( 5751) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10006 Ramachandran restraints generated. 5003 Oldfield, 0 Emsley, 5003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 194 time to evaluate : 1.555 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: O 105 MET cc_start: 0.5715 (mmp) cc_final: 0.5109 (ptm) REVERT: H 61 ASN cc_start: 0.7909 (p0) cc_final: 0.7592 (m-40) REVERT: A 297 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.8720 (t80) REVERT: A 312 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8199 (mpp) REVERT: A 607 MET cc_start: 0.9160 (ptt) cc_final: 0.8872 (ppp) REVERT: B 108 MET cc_start: 0.7967 (mtt) cc_final: 0.7706 (mtt) REVERT: B 289 ARG cc_start: 0.9400 (OUTLIER) cc_final: 0.9116 (ptp-110) REVERT: B 337 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8810 (mtp) REVERT: B 383 MET cc_start: 0.9085 (tpp) cc_final: 0.8716 (tpp) REVERT: C 324 MET cc_start: 0.8587 (mmp) cc_final: 0.8243 (mpp) REVERT: C 604 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9007 (tt) REVERT: C 607 MET cc_start: 0.9304 (ptm) cc_final: 0.8728 (ppp) REVERT: D 150 MET cc_start: 0.8965 (tmm) cc_final: 0.8207 (tmm) REVERT: D 151 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9030 (tp) REVERT: D 383 MET cc_start: 0.8942 (ttp) cc_final: 0.8581 (ttp) REVERT: E 312 MET cc_start: 0.9119 (mmm) cc_final: 0.8798 (mmm) REVERT: E 324 MET cc_start: 0.9375 (mtt) cc_final: 0.8806 (mtt) REVERT: E 348 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.9014 (mtpp) REVERT: E 352 MET cc_start: 0.8793 (tmm) cc_final: 0.8361 (tmm) REVERT: E 482 ARG cc_start: 0.9319 (OUTLIER) cc_final: 0.8854 (ptp90) REVERT: F 215 MET cc_start: 0.9164 (pmm) cc_final: 0.8944 (pmm) REVERT: F 230 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8591 (tp30) REVERT: M 118 ASN cc_start: 0.6533 (p0) cc_final: 0.6044 (m-40) REVERT: N 47 LYS cc_start: 0.6894 (tmtt) cc_final: 0.6400 (mmmt) REVERT: I 157 MET cc_start: 0.8452 (mmt) cc_final: 0.7804 (mmt) REVERT: J 18 HIS cc_start: 0.8501 (m90) cc_final: 0.8130 (m170) REVERT: J 53 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7614 (pp20) REVERT: P 91 ARG cc_start: 0.8442 (tpt170) cc_final: 0.7647 (tpm170) REVERT: P 224 MET cc_start: 0.8798 (mmp) cc_final: 0.8538 (mmp) REVERT: P 236 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7633 (p0) outliers start: 71 outliers final: 55 residues processed: 254 average time/residue: 0.2101 time to fit residues: 89.9371 Evaluate side-chains 250 residues out of total 4323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 185 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 202 LEU Chi-restraints excluded: chain O residue 210 TYR Chi-restraints excluded: chain G residue 50 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 297 PHE Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 451 PHE Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain E residue 142 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 251 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 348 LYS Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain E residue 482 ARG Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 532 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 398 ASP Chi-restraints excluded: chain K residue 51 VAL Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 101 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 53 LYS Chi-restraints excluded: chain N residue 59 GLU Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 70 MET Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 80 LEU Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 166 LEU Chi-restraints excluded: chain P residue 236 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 279 optimal weight: 5.9990 chunk 272 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 476 optimal weight: 0.5980 chunk 408 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 223 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 301 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 442 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 GLN ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 ASN ** 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 = 0.3503 r_free = 0.3503 target = 0.067855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046778 restraints weight = 220722.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.047688 restraints weight = 121609.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.048265 restraints weight = 81645.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.048634 restraints weight = 63935.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.048881 restraints weight = 55494.011| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 40247 Z= 0.153 Angle : 0.615 15.479 54373 Z= 0.318 Chirality : 0.043 0.219 6136 Planarity : 0.004 0.050 7056 Dihedral : 4.472 37.778 5459 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.74 % Allowed : 15.95 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.38 % 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: -0.16 (0.12), residues: 5003 helix: 1.40 (0.11), residues: 2246 sheet: -1.58 (0.21), residues: 585 loop : -1.28 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 146 TYR 0.026 0.001 TYR I 43 PHE 0.034 0.001 PHE K 62 TRP 0.043 0.001 TRP A 567 HIS 0.006 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00341 (40247) covalent geometry : angle 0.61485 (54373) hydrogen bonds : bond 0.04134 ( 1992) hydrogen bonds : angle 4.60255 ( 5751) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7064.00 seconds wall clock time: 123 minutes 5.21 seconds (7385.21 seconds total)