Starting phenix.real_space_refine on Sun Feb 18 06:35:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2g_8962/02_2024/6e2g_8962.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2g_8962/02_2024/6e2g_8962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2g_8962/02_2024/6e2g_8962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2g_8962/02_2024/6e2g_8962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2g_8962/02_2024/6e2g_8962.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2g_8962/02_2024/6e2g_8962.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.006 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 149 5.16 5 C 13616 2.51 5 N 3553 2.21 5 O 3784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A ARG 620": "NH1" <-> "NH2" Residue "A ARG 635": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ARG 614": "NH1" <-> "NH2" Residue "B ARG 620": "NH1" <-> "NH2" Residue "B ARG 635": "NH1" <-> "NH2" Residue "B ARG 642": "NH1" <-> "NH2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 262": "NH1" <-> "NH2" Residue "C ARG 354": "NH1" <-> "NH2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C ARG 614": "NH1" <-> "NH2" Residue "C ARG 620": "NH1" <-> "NH2" Residue "C ARG 635": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D ARG 354": "NH1" <-> "NH2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 614": "NH1" <-> "NH2" Residue "D ARG 620": "NH1" <-> "NH2" Residue "D ARG 635": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21108 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4885 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 25, 'TRANS': 585} Chain: "B" Number of atoms: 4979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4979 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 25, 'TRANS': 595} Chain: "C" Number of atoms: 5172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5172 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 25, 'TRANS': 618} Chain breaks: 1 Chain: "D" Number of atoms: 4901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4901 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 25, 'TRANS': 587} Chain: "E" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1165 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 11.11, per 1000 atoms: 0.53 Number of scatterers: 21108 At special positions: 0 Unit cell: (133.56, 130.38, 131.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 149 16.00 O 3784 8.00 N 3553 7.00 C 13616 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 - 3.50 Amino acid : False - 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: 7.47 Conformation dependent library (CDL) restraints added in 3.5 seconds 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4946 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 8 sheets defined 58.9% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 27 through 44 removed outlier: 4.470A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.753A pdb=" N LEU A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.545A pdb=" N TYR A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.653A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.738A pdb=" N PHE A 107 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 4.094A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.595A pdb=" N PHE A 169 " --> pdb=" O HIS A 165 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 170 " --> pdb=" O PRO A 166 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.871A pdb=" N ILE A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.565A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.823A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 234 removed outlier: 3.564A pdb=" N VAL A 234 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 252 through 260 removed outlier: 3.533A pdb=" N MET A 259 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 296 removed outlier: 4.238A pdb=" N VAL A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.597A pdb=" N ARG A 304 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 307 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 308 " --> pdb=" O GLN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 322 removed outlier: 3.693A pdb=" N TRP A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 347 removed outlier: 3.544A pdb=" N PHE A 328 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N CYS A 345 " --> pdb=" O CYS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 402 removed outlier: 3.779A pdb=" N GLY A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A 395 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.004A pdb=" N ILE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 442 removed outlier: 3.922A pdb=" N VAL A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 430 " --> pdb=" O VAL A 426 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 463 removed outlier: 3.691A pdb=" N PHE A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 457 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 474 through 486 removed outlier: 3.731A pdb=" N THR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 479 " --> pdb=" O GLY A 475 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 486 " --> pdb=" O GLN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 removed outlier: 3.647A pdb=" N VAL A 498 " --> pdb=" O TRP A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 511 removed outlier: 3.548A pdb=" N ALA A 504 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.555A pdb=" N THR A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 569 removed outlier: 4.078A pdb=" N ALA A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 582 removed outlier: 4.279A pdb=" N ALA A 575 " --> pdb=" O ASN A 571 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 580 " --> pdb=" O MET A 576 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TRP A 582 " --> pdb=" O GLY A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 605 removed outlier: 3.605A pdb=" N LEU A 591 " --> pdb=" O GLU A 587 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG A 593 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 597 " --> pdb=" O ARG A 593 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A 605 " --> pdb=" O VAL A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 44 removed outlier: 3.719A pdb=" N ASP B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.978A pdb=" N LEU B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.873A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 removed outlier: 4.203A pdb=" N PHE B 107 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 4.240A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 165 through 171 removed outlier: 3.824A pdb=" N ALA B 170 " --> pdb=" O PRO B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.763A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.533A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.992A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 250 removed outlier: 3.819A pdb=" N GLY B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 290 through 296 removed outlier: 3.770A pdb=" N VAL B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.905A pdb=" N ALA B 303 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLN B 305 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 307 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP B 308 " --> pdb=" O GLN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 removed outlier: 4.030A pdb=" N TRP B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 3.555A pdb=" N TYR B 327 " --> pdb=" O TYR B 323 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS B 345 " --> pdb=" O CYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 403 removed outlier: 3.774A pdb=" N VAL B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.578A pdb=" N ARG B 408 " --> pdb=" O PRO B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 442 removed outlier: 3.634A pdb=" N ILE B 427 " --> pdb=" O PRO B 423 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 462 removed outlier: 3.594A pdb=" N PHE B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 removed outlier: 3.748A pdb=" N GLY B 470 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE B 471 " --> pdb=" O ALA B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 486 removed outlier: 3.813A pdb=" N THR B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE B 479 " --> pdb=" O GLY B 475 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 486 " --> pdb=" O GLN B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 511 removed outlier: 4.184A pdb=" N LEU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY B 502 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 537 removed outlier: 3.584A pdb=" N LEU B 529 " --> pdb=" O TYR B 525 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B 530 " --> pdb=" O PRO B 526 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 537 " --> pdb=" O PHE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 565 removed outlier: 3.859A pdb=" N SER B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 556 " --> pdb=" O PHE B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 582 removed outlier: 4.113A pdb=" N ALA B 575 " --> pdb=" O ASN B 571 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TRP B 582 " --> pdb=" O GLY B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 605 removed outlier: 3.557A pdb=" N ARG B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 597 " --> pdb=" O ARG B 593 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET B 602 " --> pdb=" O ALA B 598 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 645 removed outlier: 3.832A pdb=" N ILE B 643 " --> pdb=" O ASN B 639 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 644 " --> pdb=" O ARG B 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.701A pdb=" N ASP C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.807A pdb=" N LEU C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.518A pdb=" N LEU C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.520A pdb=" N ALA C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.673A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.818A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 removed outlier: 3.590A pdb=" N ALA C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.584A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.608A pdb=" N LEU C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 removed outlier: 3.504A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 204' Processing helix chain 'C' and resid 211 through 223 removed outlier: 4.151A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.792A pdb=" N GLY C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 3.556A pdb=" N GLN C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 296 removed outlier: 3.894A pdb=" N VAL C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 removed outlier: 4.290A pdb=" N GLN C 305 " --> pdb=" O GLU C 302 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 307 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP C 308 " --> pdb=" O GLN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 322 removed outlier: 3.734A pdb=" N TRP C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 347 removed outlier: 3.631A pdb=" N TYR C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 338 " --> pdb=" O ILE C 334 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS C 345 " --> pdb=" O CYS C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 407 removed outlier: 3.568A pdb=" N LEU C 385 " --> pdb=" O ASP C 381 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 386 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY C 387 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER C 391 " --> pdb=" O GLY C 387 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix removed outlier: 3.877A pdb=" N PHE C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 425 Processing helix chain 'C' and resid 426 through 442 removed outlier: 4.164A pdb=" N LEU C 436 " --> pdb=" O ALA C 432 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR C 438 " --> pdb=" O MET C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 462 removed outlier: 3.517A pdb=" N VAL C 458 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS C 462 " --> pdb=" O VAL C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 469 removed outlier: 3.592A pdb=" N TYR C 466 " --> pdb=" O ASN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 489 removed outlier: 3.801A pdb=" N THR C 478 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 479 " --> pdb=" O GLY C 475 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET C 480 " --> pdb=" O PRO C 476 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 486 " --> pdb=" O GLN C 482 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLY C 487 " --> pdb=" O LYS C 483 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU C 489 " --> pdb=" O ILE C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 511 removed outlier: 4.914A pdb=" N LEU C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL C 498 " --> pdb=" O TRP C 494 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 504 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 510 " --> pdb=" O ALA C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 524 through 534 removed outlier: 4.381A pdb=" N PHE C 530 " --> pdb=" O PRO C 526 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 566 removed outlier: 3.978A pdb=" N SER C 555 " --> pdb=" O PRO C 551 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE C 556 " --> pdb=" O PHE C 552 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 582 removed outlier: 4.126A pdb=" N ALA C 575 " --> pdb=" O ASN C 571 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TRP C 582 " --> pdb=" O GLY C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 607 removed outlier: 3.535A pdb=" N LEU C 603 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 604 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 605 " --> pdb=" O VAL C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 651 removed outlier: 3.654A pdb=" N ALA C 649 " --> pdb=" O ARG C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 705 removed outlier: 3.658A pdb=" N ASN C 696 " --> pdb=" O ARG C 692 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 705 " --> pdb=" O ARG C 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 46 removed outlier: 3.684A pdb=" N SER D 32 " --> pdb=" O SER D 28 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.649A pdb=" N LEU D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 64 removed outlier: 3.647A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.516A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 removed outlier: 3.530A pdb=" N ALA D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.517A pdb=" N ALA D 170 " --> pdb=" O PRO D 166 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.548A pdb=" N ILE D 183 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.832A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 221 removed outlier: 3.763A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 219 " --> pdb=" O MET D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.745A pdb=" N GLY D 247 " --> pdb=" O PHE D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 removed outlier: 3.550A pdb=" N GLN D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 296 removed outlier: 3.759A pdb=" N VAL D 296 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 309 removed outlier: 3.888A pdb=" N ARG D 304 " --> pdb=" O ARG D 301 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN D 305 " --> pdb=" O GLU D 302 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE D 306 " --> pdb=" O ALA D 303 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU D 307 " --> pdb=" O ARG D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 322 removed outlier: 3.802A pdb=" N LEU D 315 " --> pdb=" O PRO D 311 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER D 317 " --> pdb=" O LYS D 313 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 345 removed outlier: 3.721A pdb=" N TYR D 327 " --> pdb=" O TYR D 323 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 407 removed outlier: 3.524A pdb=" N VAL D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA D 395 " --> pdb=" O SER D 391 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL D 396 " --> pdb=" O ILE D 392 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) Proline residue: D 404 - end of helix Processing helix chain 'D' and resid 422 through 425 removed outlier: 3.559A pdb=" N HIS D 425 " --> pdb=" O GLY D 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 422 through 425' Processing helix chain 'D' and resid 426 through 442 removed outlier: 3.635A pdb=" N THR D 430 " --> pdb=" O VAL D 426 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU D 436 " --> pdb=" O ALA D 432 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D 437 " --> pdb=" O PHE D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 461 removed outlier: 4.107A pdb=" N MET D 453 " --> pdb=" O GLU D 449 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D 455 " --> pdb=" O VAL D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'D' and resid 474 through 486 removed outlier: 3.805A pdb=" N THR D 478 " --> pdb=" O LEU D 474 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE D 479 " --> pdb=" O GLY D 475 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET D 480 " --> pdb=" O PRO D 476 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 511 removed outlier: 4.016A pdb=" N VAL D 498 " --> pdb=" O TRP D 494 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE D 510 " --> pdb=" O ALA D 506 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE D 511 " --> pdb=" O PHE D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 537 removed outlier: 4.064A pdb=" N PHE D 530 " --> pdb=" O PRO D 526 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU D 534 " --> pdb=" O PHE D 530 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 537 " --> pdb=" O PHE D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 567 removed outlier: 4.155A pdb=" N SER D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE D 556 " --> pdb=" O PHE D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 583 removed outlier: 4.483A pdb=" N ALA D 575 " --> pdb=" O ASN D 571 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP D 582 " --> pdb=" O GLY D 578 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG D 583 " --> pdb=" O ASP D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 605 removed outlier: 3.948A pdb=" N ARG D 593 " --> pdb=" O ASP D 589 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 603 " --> pdb=" O THR D 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 20 removed outlier: 3.621A pdb=" N ILE E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU E 11 " --> pdb=" O GLU E 7 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 38 removed outlier: 3.918A pdb=" N VAL E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 56 removed outlier: 3.581A pdb=" N VAL E 55 " --> pdb=" O MET E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 75 removed outlier: 3.731A pdb=" N ARG E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 93 removed outlier: 3.875A pdb=" N ARG E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.527A pdb=" N ARG E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N HIS E 107 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 127 removed outlier: 3.608A pdb=" N ASP E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 143 removed outlier: 3.727A pdb=" N GLN E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 269 removed outlier: 7.295A pdb=" N SER A 274 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR A 268 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 352 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 269 removed outlier: 6.916A pdb=" N SER B 274 " --> pdb=" O GLN B 266 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N THR B 268 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 351 through 353 Processing sheet with id=AA5, first strand: chain 'C' and resid 263 through 269 removed outlier: 5.065A pdb=" N ILE C 265 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU C 276 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TRP C 267 " --> pdb=" O SER C 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 351 through 352 Processing sheet with id=AA7, first strand: chain 'D' and resid 263 through 269 removed outlier: 6.956A pdb=" N SER D 274 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR D 268 " --> pdb=" O LEU D 272 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU D 272 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR D 273 " --> pdb=" O ASP D 634 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU D 630 " --> pdb=" O TYR D 277 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 351 through 353 795 hydrogen bonds defined for protein. 2268 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: 5.70 Time building geometry restraints manager: 8.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6165 1.33 - 1.45: 3815 1.45 - 1.57: 11336 1.57 - 1.69: 0 1.69 - 1.81: 254 Bond restraints: 21570 Sorted by residual: bond pdb=" C LYS A 606 " pdb=" N LEU A 607 " ideal model delta sigma weight residual 1.331 1.230 0.101 2.83e-02 1.25e+03 1.28e+01 bond pdb=" C GLU A 164 " pdb=" N HIS A 165 " ideal model delta sigma weight residual 1.331 1.245 0.086 2.83e-02 1.25e+03 9.31e+00 bond pdb=" C ILE A 403 " pdb=" N PRO A 404 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.39e+00 bond pdb=" CB ARG D 469 " pdb=" CG ARG D 469 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.72e+00 bond pdb=" C VAL D 451 " pdb=" N PRO D 452 " ideal model delta sigma weight residual 1.336 1.361 -0.025 1.20e-02 6.94e+03 4.44e+00 ... (remaining 21565 not shown) Histogram of bond angle deviations from ideal: 97.69 - 105.11: 435 105.11 - 112.53: 10832 112.53 - 119.95: 8732 119.95 - 127.37: 9016 127.37 - 134.79: 247 Bond angle restraints: 29262 Sorted by residual: angle pdb=" C ASP B 637 " pdb=" N LEU B 638 " pdb=" CA LEU B 638 " ideal model delta sigma weight residual 121.54 134.79 -13.25 1.91e+00 2.74e-01 4.81e+01 angle pdb=" C LYS C 209 " pdb=" N THR C 210 " pdb=" CA THR C 210 " ideal model delta sigma weight residual 121.54 132.15 -10.61 1.91e+00 2.74e-01 3.09e+01 angle pdb=" N PHE A 211 " pdb=" CA PHE A 211 " pdb=" C PHE A 211 " ideal model delta sigma weight residual 114.75 108.13 6.62 1.26e+00 6.30e-01 2.76e+01 angle pdb=" N PHE D 211 " pdb=" CA PHE D 211 " pdb=" C PHE D 211 " ideal model delta sigma weight residual 114.75 108.24 6.51 1.26e+00 6.30e-01 2.67e+01 angle pdb=" N THR B 310 " pdb=" CA THR B 310 " pdb=" C THR B 310 " ideal model delta sigma weight residual 109.81 121.13 -11.32 2.21e+00 2.05e-01 2.62e+01 ... (remaining 29257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 11986 17.49 - 34.99: 719 34.99 - 52.48: 141 52.48 - 69.97: 11 69.97 - 87.47: 12 Dihedral angle restraints: 12869 sinusoidal: 5192 harmonic: 7677 Sorted by residual: dihedral pdb=" CA GLY B 286 " pdb=" C GLY B 286 " pdb=" N ASP B 287 " pdb=" CA ASP B 287 " ideal model delta harmonic sigma weight residual 180.00 -131.18 -48.82 0 5.00e+00 4.00e-02 9.53e+01 dihedral pdb=" CA ARG C 362 " pdb=" C ARG C 362 " pdb=" N ASP C 363 " pdb=" CA ASP C 363 " ideal model delta harmonic sigma weight residual 180.00 140.49 39.51 0 5.00e+00 4.00e-02 6.25e+01 dihedral pdb=" CA LYS C 209 " pdb=" C LYS C 209 " pdb=" N THR C 210 " pdb=" CA THR C 210 " ideal model delta harmonic sigma weight residual 180.00 141.98 38.02 0 5.00e+00 4.00e-02 5.78e+01 ... (remaining 12866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2713 0.079 - 0.157: 539 0.157 - 0.235: 58 0.235 - 0.314: 10 0.314 - 0.392: 1 Chirality restraints: 3321 Sorted by residual: chirality pdb=" CB ILE E 100 " pdb=" CA ILE E 100 " pdb=" CG1 ILE E 100 " pdb=" CG2 ILE E 100 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA THR B 310 " pdb=" N THR B 310 " pdb=" C THR B 310 " pdb=" CB THR B 310 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CB ILE A 355 " pdb=" CA ILE A 355 " pdb=" CG1 ILE A 355 " pdb=" CG2 ILE A 355 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 3318 not shown) Planarity restraints: 3721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 286 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C GLY B 286 " 0.067 2.00e-02 2.50e+03 pdb=" O GLY B 286 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP B 287 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 612 " -0.021 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRP C 612 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP C 612 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 612 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 612 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 612 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 612 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 612 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 612 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP C 612 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 403 " 0.048 5.00e-02 4.00e+02 7.11e-02 8.10e+00 pdb=" N PRO D 404 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 404 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 404 " 0.040 5.00e-02 4.00e+02 ... (remaining 3718 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5219 2.78 - 3.31: 19522 3.31 - 3.84: 33101 3.84 - 4.37: 38798 4.37 - 4.90: 64150 Nonbonded interactions: 160790 Sorted by model distance: nonbonded pdb=" OG SER D 505 " pdb=" OH TYR D 525 " model vdw 2.249 2.440 nonbonded pdb=" O VAL B 151 " pdb=" ND2 ASN B 158 " model vdw 2.270 2.520 nonbonded pdb=" NH1 ARG B 469 " pdb=" OE1 GLN B 595 " model vdw 2.283 2.520 nonbonded pdb=" O VAL A 440 " pdb=" OG1 THR A 444 " model vdw 2.291 2.440 nonbonded pdb=" OD1 ASP A 34 " pdb=" NH1 ARG D 631 " model vdw 2.298 2.520 ... (remaining 160785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 637) selection = (chain 'B' and resid 27 through 637) selection = (chain 'C' and resid 27 through 637) selection = (chain 'D' and resid 27 through 637) } 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.460 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 51.230 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.010 0.106 21570 Z= 0.634 Angle : 1.212 16.361 29262 Z= 0.629 Chirality : 0.064 0.392 3321 Planarity : 0.007 0.071 3721 Dihedral : 11.958 87.467 7923 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.42 % Allowed : 12.38 % Favored : 87.20 % Rotamer: Outliers : 1.05 % Allowed : 7.42 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.78 (0.12), residues: 2625 helix: -4.05 (0.07), residues: 1393 sheet: -1.74 (0.61), residues: 80 loop : -3.60 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP C 612 HIS 0.013 0.002 HIS B 157 PHE 0.026 0.004 PHE B 552 TYR 0.028 0.003 TYR D 523 ARG 0.015 0.001 ARG D 631 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 497 time to evaluate : 2.519 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: A 99 MET cc_start: 0.8572 (mtm) cc_final: 0.8134 (mtm) REVERT: A 219 LEU cc_start: 0.9388 (mm) cc_final: 0.8976 (mp) REVERT: A 278 ASP cc_start: 0.8132 (t0) cc_final: 0.7884 (t0) REVERT: A 289 GLN cc_start: 0.8727 (mt0) cc_final: 0.8377 (pm20) REVERT: A 344 MET cc_start: 0.8057 (mtt) cc_final: 0.7651 (mmp) REVERT: A 455 PHE cc_start: 0.8619 (m-10) cc_final: 0.8080 (m-80) REVERT: A 484 MET cc_start: 0.7996 (mmt) cc_final: 0.7665 (mmt) REVERT: A 494 TRP cc_start: 0.8442 (m100) cc_final: 0.8094 (m100) REVERT: A 590 GLU cc_start: 0.8101 (tp30) cc_final: 0.7511 (tp30) REVERT: B 301 ARG cc_start: 0.8697 (ttt-90) cc_final: 0.8428 (tpt90) REVERT: B 434 MET cc_start: 0.8979 (mmt) cc_final: 0.8122 (mmm) REVERT: B 484 MET cc_start: 0.8600 (mmt) cc_final: 0.8169 (mmt) REVERT: B 547 ASP cc_start: 0.8488 (m-30) cc_final: 0.8203 (t0) REVERT: B 572 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8823 (tm) REVERT: B 602 MET cc_start: 0.8261 (tmm) cc_final: 0.7941 (tmm) REVERT: B 641 GLN cc_start: 0.8701 (tt0) cc_final: 0.8181 (tm-30) REVERT: C 110 MET cc_start: 0.9287 (mtt) cc_final: 0.9005 (mtp) REVERT: C 113 GLU cc_start: 0.9133 (tp30) cc_final: 0.8907 (tm-30) REVERT: C 237 ASN cc_start: 0.8894 (t160) cc_final: 0.8638 (m110) REVERT: C 281 GLU cc_start: 0.8170 (tp30) cc_final: 0.7959 (tm-30) REVERT: C 283 ASP cc_start: 0.7737 (t0) cc_final: 0.6906 (t0) REVERT: C 300 LYS cc_start: 0.9027 (mtpm) cc_final: 0.8815 (ttmt) REVERT: C 301 ARG cc_start: 0.8131 (ttt-90) cc_final: 0.7815 (tpt90) REVERT: C 441 MET cc_start: 0.8828 (mmt) cc_final: 0.8544 (mmm) REVERT: C 473 MET cc_start: 0.8696 (ttt) cc_final: 0.7632 (ptp) REVERT: C 576 MET cc_start: 0.9221 (tpt) cc_final: 0.8758 (tpp) REVERT: C 595 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8456 (mm-40) REVERT: D 65 LEU cc_start: 0.9325 (mt) cc_final: 0.9095 (mt) REVERT: D 78 MET cc_start: 0.8740 (mpt) cc_final: 0.8026 (mpt) REVERT: D 176 GLU cc_start: 0.8588 (pt0) cc_final: 0.8375 (pp20) REVERT: D 233 LEU cc_start: 0.8796 (mm) cc_final: 0.8450 (mp) REVERT: D 293 GLU cc_start: 0.8929 (tp30) cc_final: 0.8541 (tp30) REVERT: D 301 ARG cc_start: 0.8987 (tpp-160) cc_final: 0.8724 (tpp80) REVERT: D 322 ARG cc_start: 0.9025 (mtm180) cc_final: 0.8337 (tpt170) REVERT: D 389 LEU cc_start: 0.9471 (mm) cc_final: 0.9157 (mm) REVERT: E 14 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8532 (mm-30) REVERT: E 34 THR cc_start: 0.7952 (p) cc_final: 0.7714 (t) REVERT: E 39 LEU cc_start: 0.8842 (tt) cc_final: 0.8579 (tt) REVERT: E 77 LYS cc_start: 0.6736 (mmpt) cc_final: 0.5907 (mmtt) REVERT: E 144 MET cc_start: 0.8332 (mmm) cc_final: 0.8037 (mmt) outliers start: 24 outliers final: 7 residues processed: 516 average time/residue: 0.3493 time to fit residues: 268.1350 Evaluate side-chains 301 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 293 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 612 TRP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 611 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 67 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 205 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 237 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 118 GLN A 217 ASN A 237 ASN A 251 ASN A 364 ASN A 571 ASN ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 122 HIS B 237 ASN B 251 ASN ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 ASN B 368 GLN B 581 HIS B 586 HIS C 37 ASN C 118 GLN C 237 ASN C 251 ASN ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 HIS ** C 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN D 251 ASN D 445 ASN D 482 GLN D 571 ASN D 581 HIS E 8 GLN ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 21570 Z= 0.206 Angle : 0.748 16.706 29262 Z= 0.376 Chirality : 0.043 0.191 3321 Planarity : 0.004 0.050 3721 Dihedral : 6.830 53.295 2893 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.02 % Favored : 89.75 % Rotamer: Outliers : 3.07 % Allowed : 12.64 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.14), residues: 2625 helix: -2.21 (0.11), residues: 1454 sheet: -1.71 (0.55), residues: 87 loop : -3.23 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 612 HIS 0.010 0.001 HIS C 586 PHE 0.024 0.002 PHE E 65 TYR 0.014 0.001 TYR D 523 ARG 0.006 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 380 time to evaluate : 2.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9208 (tm) REVERT: A 110 MET cc_start: 0.8473 (mtt) cc_final: 0.8201 (mmt) REVERT: A 275 THR cc_start: 0.9021 (m) cc_final: 0.8722 (p) REVERT: A 278 ASP cc_start: 0.8234 (t0) cc_final: 0.7329 (t70) REVERT: A 289 GLN cc_start: 0.8543 (mt0) cc_final: 0.8208 (pm20) REVERT: A 344 MET cc_start: 0.8136 (mtt) cc_final: 0.7621 (mmt) REVERT: A 388 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8086 (tt0) REVERT: A 473 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8334 (ppp) REVERT: A 500 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8812 (tt) REVERT: A 576 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8057 (ttt) REVERT: A 595 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8124 (mm110) REVERT: B 96 MET cc_start: 0.8497 (tmm) cc_final: 0.8190 (tmm) REVERT: B 110 MET cc_start: 0.9008 (mtp) cc_final: 0.8659 (mtp) REVERT: B 314 GLU cc_start: 0.7674 (mp0) cc_final: 0.7343 (mp0) REVERT: B 490 MET cc_start: 0.7910 (mmm) cc_final: 0.7682 (mmm) REVERT: B 547 ASP cc_start: 0.8314 (m-30) cc_final: 0.7771 (t0) REVERT: B 590 GLU cc_start: 0.8700 (tp30) cc_final: 0.8247 (tp30) REVERT: B 602 MET cc_start: 0.8323 (tmm) cc_final: 0.8025 (tmm) REVERT: B 611 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8641 (pp) REVERT: B 641 GLN cc_start: 0.8683 (tt0) cc_final: 0.8288 (tp40) REVERT: C 61 LEU cc_start: 0.9201 (mt) cc_final: 0.8986 (mt) REVERT: C 113 GLU cc_start: 0.9073 (tp30) cc_final: 0.8860 (tm-30) REVERT: C 215 MET cc_start: 0.8520 (tpp) cc_final: 0.8290 (tpp) REVERT: C 283 ASP cc_start: 0.7619 (t0) cc_final: 0.6806 (t0) REVERT: C 288 ASP cc_start: 0.8266 (m-30) cc_final: 0.7955 (t0) REVERT: C 304 ARG cc_start: 0.8677 (ttp-170) cc_final: 0.8351 (mtp-110) REVERT: C 441 MET cc_start: 0.8791 (mmt) cc_final: 0.8554 (mmm) REVERT: C 473 MET cc_start: 0.8753 (ttt) cc_final: 0.7658 (ptp) REVERT: C 576 MET cc_start: 0.8997 (tpt) cc_final: 0.8666 (tpp) REVERT: C 589 ASP cc_start: 0.8447 (m-30) cc_final: 0.8205 (p0) REVERT: D 65 LEU cc_start: 0.9299 (mt) cc_final: 0.9091 (mt) REVERT: D 78 MET cc_start: 0.8701 (mpt) cc_final: 0.7991 (mpt) REVERT: D 99 MET cc_start: 0.9152 (mtm) cc_final: 0.8630 (mtm) REVERT: D 293 GLU cc_start: 0.8875 (tp30) cc_final: 0.8478 (tp30) REVERT: D 308 ASP cc_start: 0.8250 (m-30) cc_final: 0.7929 (m-30) REVERT: D 315 LEU cc_start: 0.9107 (mp) cc_final: 0.8800 (mp) REVERT: D 322 ARG cc_start: 0.8916 (mtm180) cc_final: 0.8412 (tpt170) REVERT: D 482 GLN cc_start: 0.8673 (tm-30) cc_final: 0.7823 (mm-40) REVERT: D 553 MET cc_start: 0.8067 (tpp) cc_final: 0.7751 (tpp) REVERT: D 571 ASN cc_start: 0.8920 (m-40) cc_final: 0.8639 (m110) REVERT: E 51 MET cc_start: 0.8902 (ttm) cc_final: 0.8200 (ttm) REVERT: E 144 MET cc_start: 0.8286 (mmm) cc_final: 0.7728 (mmt) outliers start: 70 outliers final: 32 residues processed: 431 average time/residue: 0.3171 time to fit residues: 211.8717 Evaluate side-chains 319 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 282 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 612 TRP Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 572 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain D residue 539 ILE Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 101 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 162 optimal weight: 0.0670 chunk 65 optimal weight: 6.9990 chunk 238 optimal weight: 0.0020 chunk 257 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 236 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 overall best weight: 2.6132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 118 GLN A 122 HIS A 369 GLN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 586 HIS ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN D 369 GLN E 8 GLN ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21570 Z= 0.254 Angle : 0.723 16.177 29262 Z= 0.359 Chirality : 0.043 0.179 3321 Planarity : 0.004 0.044 3721 Dihedral : 6.228 47.135 2890 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.12 % Favored : 88.61 % Rotamer: Outliers : 3.73 % Allowed : 15.14 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.15), residues: 2625 helix: -1.11 (0.13), residues: 1464 sheet: -1.30 (0.57), residues: 81 loop : -3.17 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 612 HIS 0.005 0.001 HIS B 157 PHE 0.015 0.002 PHE E 16 TYR 0.018 0.001 TYR B 338 ARG 0.009 0.000 ARG E 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 310 time to evaluate : 2.399 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: A 39 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9044 (tm) REVERT: A 96 MET cc_start: 0.8847 (ptp) cc_final: 0.8633 (ptp) REVERT: A 275 THR cc_start: 0.9069 (m) cc_final: 0.8761 (p) REVERT: A 289 GLN cc_start: 0.8582 (mt0) cc_final: 0.8237 (pm20) REVERT: A 344 MET cc_start: 0.8021 (mtt) cc_final: 0.7654 (mmt) REVERT: A 382 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8689 (p0) REVERT: A 473 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8570 (ppp) REVERT: A 500 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8847 (tt) REVERT: A 501 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8453 (mm) REVERT: A 576 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8472 (ttt) REVERT: A 590 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7708 (mm-30) REVERT: A 595 GLN cc_start: 0.8717 (mm-40) cc_final: 0.8333 (mm110) REVERT: B 96 MET cc_start: 0.8606 (tmm) cc_final: 0.8310 (tmm) REVERT: B 110 MET cc_start: 0.8858 (mtp) cc_final: 0.8517 (mtp) REVERT: B 176 GLU cc_start: 0.8896 (pt0) cc_final: 0.8642 (pp20) REVERT: B 259 MET cc_start: 0.8982 (tpp) cc_final: 0.8562 (tpp) REVERT: B 275 THR cc_start: 0.8884 (m) cc_final: 0.8438 (p) REVERT: B 301 ARG cc_start: 0.7658 (tpt90) cc_final: 0.7436 (tpt90) REVERT: B 399 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8986 (mm) REVERT: B 401 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8468 (p) REVERT: B 547 ASP cc_start: 0.8331 (m-30) cc_final: 0.7946 (t0) REVERT: B 590 GLU cc_start: 0.8694 (tp30) cc_final: 0.8247 (tp30) REVERT: B 595 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8119 (mm-40) REVERT: B 602 MET cc_start: 0.8268 (tmm) cc_final: 0.8061 (tmm) REVERT: B 641 GLN cc_start: 0.8632 (tt0) cc_final: 0.8278 (tp40) REVERT: C 31 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7776 (pm20) REVERT: C 113 GLU cc_start: 0.9089 (tp30) cc_final: 0.8865 (tm-30) REVERT: C 193 ASP cc_start: 0.8252 (p0) cc_final: 0.8016 (p0) REVERT: C 237 ASN cc_start: 0.8857 (t0) cc_final: 0.8499 (m110) REVERT: C 283 ASP cc_start: 0.7597 (t0) cc_final: 0.6820 (t0) REVERT: C 473 MET cc_start: 0.8744 (ttt) cc_final: 0.7684 (ptp) REVERT: C 495 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9094 (mm) REVERT: C 589 ASP cc_start: 0.8535 (m-30) cc_final: 0.8332 (p0) REVERT: D 78 MET cc_start: 0.8715 (mpt) cc_final: 0.7950 (mpt) REVERT: D 99 MET cc_start: 0.9201 (mtm) cc_final: 0.8938 (mtm) REVERT: D 308 ASP cc_start: 0.8371 (m-30) cc_final: 0.8053 (m-30) REVERT: D 322 ARG cc_start: 0.8940 (mtm180) cc_final: 0.8375 (tpt170) REVERT: D 553 MET cc_start: 0.8124 (tpp) cc_final: 0.7919 (tpp) REVERT: E 8 GLN cc_start: 0.8292 (mt0) cc_final: 0.8067 (mt0) REVERT: E 124 MET cc_start: 0.9382 (mtp) cc_final: 0.9158 (mtp) REVERT: E 144 MET cc_start: 0.8279 (mmm) cc_final: 0.7926 (mmm) outliers start: 85 outliers final: 48 residues processed: 371 average time/residue: 0.3138 time to fit residues: 182.8131 Evaluate side-chains 334 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 276 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 341 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 622 TYR Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 91 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 253 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 ASN B 586 HIS ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 HIS C 651 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21570 Z= 0.257 Angle : 0.705 14.809 29262 Z= 0.350 Chirality : 0.043 0.201 3321 Planarity : 0.004 0.040 3721 Dihedral : 5.856 47.276 2886 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.74 % Favored : 88.95 % Rotamer: Outliers : 4.57 % Allowed : 16.42 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.16), residues: 2625 helix: -0.53 (0.13), residues: 1455 sheet: -1.31 (0.57), residues: 83 loop : -3.09 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 612 HIS 0.006 0.001 HIS C 586 PHE 0.019 0.001 PHE B 530 TYR 0.015 0.001 TYR B 338 ARG 0.008 0.000 ARG E 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 293 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9092 (tm) REVERT: A 96 MET cc_start: 0.8909 (ptp) cc_final: 0.8707 (ptp) REVERT: A 110 MET cc_start: 0.8616 (mtt) cc_final: 0.8208 (mmt) REVERT: A 275 THR cc_start: 0.9078 (m) cc_final: 0.8787 (p) REVERT: A 289 GLN cc_start: 0.8571 (mt0) cc_final: 0.8315 (pm20) REVERT: A 344 MET cc_start: 0.7973 (mtt) cc_final: 0.7573 (mmt) REVERT: A 382 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8664 (p0) REVERT: A 465 MET cc_start: 0.8479 (mtp) cc_final: 0.8260 (mtp) REVERT: A 501 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8447 (mm) REVERT: A 590 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7570 (mm-30) REVERT: A 593 ARG cc_start: 0.8128 (mpt-90) cc_final: 0.7884 (mtm-85) REVERT: A 595 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8354 (mm110) REVERT: B 96 MET cc_start: 0.8720 (tmm) cc_final: 0.8450 (tmm) REVERT: B 110 MET cc_start: 0.8771 (mtp) cc_final: 0.8489 (mtp) REVERT: B 176 GLU cc_start: 0.8893 (pt0) cc_final: 0.8678 (pp20) REVERT: B 259 MET cc_start: 0.8929 (tpp) cc_final: 0.8540 (tpp) REVERT: B 275 THR cc_start: 0.8869 (m) cc_final: 0.8431 (p) REVERT: B 301 ARG cc_start: 0.7616 (tpt90) cc_final: 0.7349 (tpt90) REVERT: B 314 GLU cc_start: 0.7815 (mp0) cc_final: 0.7531 (mp0) REVERT: B 399 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8991 (mm) REVERT: B 490 MET cc_start: 0.7952 (mmm) cc_final: 0.7727 (mmm) REVERT: B 547 ASP cc_start: 0.8278 (m-30) cc_final: 0.7818 (t0) REVERT: B 590 GLU cc_start: 0.8731 (tp30) cc_final: 0.8285 (tp30) REVERT: B 595 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8152 (mm-40) REVERT: B 641 GLN cc_start: 0.8626 (tt0) cc_final: 0.8229 (tp40) REVERT: C 31 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7764 (pm20) REVERT: C 113 GLU cc_start: 0.9098 (tp30) cc_final: 0.8875 (tm-30) REVERT: C 193 ASP cc_start: 0.8190 (p0) cc_final: 0.7976 (p0) REVERT: C 283 ASP cc_start: 0.7544 (t0) cc_final: 0.6794 (t0) REVERT: C 383 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8868 (tp) REVERT: C 473 MET cc_start: 0.8778 (ttt) cc_final: 0.7698 (ptp) REVERT: C 586 HIS cc_start: 0.7678 (t70) cc_final: 0.7359 (t-170) REVERT: C 589 ASP cc_start: 0.8578 (m-30) cc_final: 0.8243 (p0) REVERT: C 595 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8438 (mm-40) REVERT: D 78 MET cc_start: 0.8701 (mpt) cc_final: 0.7965 (mpt) REVERT: D 308 ASP cc_start: 0.8401 (m-30) cc_final: 0.8083 (m-30) REVERT: D 322 ARG cc_start: 0.8898 (mtm180) cc_final: 0.8384 (tpt170) REVERT: D 391 SER cc_start: 0.9355 (t) cc_final: 0.8943 (p) REVERT: D 472 GLN cc_start: 0.5848 (OUTLIER) cc_final: 0.5326 (pm20) REVERT: D 553 MET cc_start: 0.8135 (tpp) cc_final: 0.7910 (tpp) REVERT: D 576 MET cc_start: 0.8658 (ttm) cc_final: 0.8406 (ttt) REVERT: D 602 MET cc_start: 0.8098 (ppp) cc_final: 0.7877 (ppp) REVERT: E 8 GLN cc_start: 0.8473 (mt0) cc_final: 0.8210 (mt0) REVERT: E 51 MET cc_start: 0.8722 (ttm) cc_final: 0.8261 (ttm) REVERT: E 126 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7891 (mtm110) REVERT: E 144 MET cc_start: 0.8244 (mmm) cc_final: 0.7887 (mmm) outliers start: 104 outliers final: 50 residues processed: 372 average time/residue: 0.3057 time to fit residues: 178.1183 Evaluate side-chains 333 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 275 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 622 TYR Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 126 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 104 optimal weight: 0.8980 chunk 216 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 129 optimal weight: 0.0970 chunk 227 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS C 73 HIS ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 HIS C 463 ASN ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 HIS ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 21570 Z= 0.171 Angle : 0.666 15.967 29262 Z= 0.326 Chirality : 0.041 0.193 3321 Planarity : 0.003 0.053 3721 Dihedral : 5.546 46.956 2886 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.13 % Favored : 89.60 % Rotamer: Outliers : 3.47 % Allowed : 17.95 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.16), residues: 2625 helix: -0.16 (0.14), residues: 1465 sheet: -1.18 (0.57), residues: 85 loop : -2.95 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 612 HIS 0.004 0.001 HIS B 157 PHE 0.022 0.001 PHE A 67 TYR 0.013 0.001 TYR B 338 ARG 0.008 0.000 ARG E 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 307 time to evaluate : 2.541 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: A 39 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9161 (tm) REVERT: A 99 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8195 (mmm) REVERT: A 110 MET cc_start: 0.8584 (mtt) cc_final: 0.8164 (mmt) REVERT: A 275 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8833 (p) REVERT: A 344 MET cc_start: 0.7923 (mtt) cc_final: 0.7714 (mmt) REVERT: A 382 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8652 (p0) REVERT: A 500 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8661 (tt) REVERT: A 569 MET cc_start: 0.8925 (mmt) cc_final: 0.8693 (mmt) REVERT: A 590 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7570 (mm-30) REVERT: A 595 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8307 (mm110) REVERT: A 602 MET cc_start: 0.8196 (tmm) cc_final: 0.7925 (tmm) REVERT: B 96 MET cc_start: 0.8698 (tmm) cc_final: 0.8412 (tmm) REVERT: B 110 MET cc_start: 0.8790 (mtp) cc_final: 0.8523 (mtp) REVERT: B 259 MET cc_start: 0.8921 (tpp) cc_final: 0.8520 (tpp) REVERT: B 275 THR cc_start: 0.8786 (m) cc_final: 0.8409 (p) REVERT: B 399 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8984 (mm) REVERT: B 434 MET cc_start: 0.9031 (mmt) cc_final: 0.8216 (mmm) REVERT: B 547 ASP cc_start: 0.8168 (m-30) cc_final: 0.7852 (t0) REVERT: B 590 GLU cc_start: 0.8689 (tp30) cc_final: 0.8223 (tp30) REVERT: B 641 GLN cc_start: 0.8596 (tt0) cc_final: 0.8206 (tp40) REVERT: C 283 ASP cc_start: 0.7764 (t0) cc_final: 0.7115 (t0) REVERT: C 302 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8039 (mm-30) REVERT: C 473 MET cc_start: 0.8821 (ttt) cc_final: 0.7747 (ptp) REVERT: C 586 HIS cc_start: 0.7584 (t70) cc_final: 0.7374 (t-170) REVERT: C 589 ASP cc_start: 0.8528 (m-30) cc_final: 0.8242 (p0) REVERT: D 78 MET cc_start: 0.8591 (mpt) cc_final: 0.7928 (mpt) REVERT: D 80 GLU cc_start: 0.9167 (pm20) cc_final: 0.8623 (pm20) REVERT: D 90 ASP cc_start: 0.8155 (t0) cc_final: 0.7947 (t0) REVERT: D 308 ASP cc_start: 0.8461 (m-30) cc_final: 0.8146 (m-30) REVERT: D 322 ARG cc_start: 0.8878 (mtm180) cc_final: 0.8359 (tpt170) REVERT: D 391 SER cc_start: 0.9306 (t) cc_final: 0.8827 (p) REVERT: D 441 MET cc_start: 0.9100 (tpp) cc_final: 0.8437 (mtt) REVERT: D 490 MET cc_start: 0.7976 (mmp) cc_final: 0.7647 (mmp) REVERT: D 576 MET cc_start: 0.8686 (ttm) cc_final: 0.8357 (ttt) REVERT: D 602 MET cc_start: 0.8112 (ppp) cc_final: 0.7849 (ppp) REVERT: E 74 ARG cc_start: 0.7823 (mpp80) cc_final: 0.7424 (mpp80) REVERT: E 123 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7998 (mp0) outliers start: 79 outliers final: 43 residues processed: 364 average time/residue: 0.3201 time to fit residues: 179.8251 Evaluate side-chains 315 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 265 time to evaluate : 2.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 622 TYR Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 126 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 253 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 HIS ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN D 289 GLN ** D 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21570 Z= 0.300 Angle : 0.734 16.373 29262 Z= 0.359 Chirality : 0.044 0.197 3321 Planarity : 0.004 0.047 3721 Dihedral : 5.581 47.655 2886 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.35 % Favored : 88.42 % Rotamer: Outliers : 4.30 % Allowed : 17.52 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.17), residues: 2625 helix: -0.01 (0.14), residues: 1469 sheet: -1.22 (0.57), residues: 85 loop : -2.94 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 612 HIS 0.006 0.001 HIS B 122 PHE 0.022 0.002 PHE A 67 TYR 0.015 0.001 TYR B 525 ARG 0.008 0.000 ARG E 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 265 time to evaluate : 2.457 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: A 39 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9146 (tm) REVERT: A 99 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8191 (mmm) REVERT: A 275 THR cc_start: 0.9116 (m) cc_final: 0.8843 (p) REVERT: A 344 MET cc_start: 0.7990 (mtt) cc_final: 0.7655 (mmt) REVERT: A 382 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8623 (p0) REVERT: A 500 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8743 (tt) REVERT: A 501 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8332 (mm) REVERT: A 590 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 595 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8380 (mm110) REVERT: B 96 MET cc_start: 0.8767 (tmm) cc_final: 0.8488 (tmm) REVERT: B 110 MET cc_start: 0.8777 (mtp) cc_final: 0.8543 (mtp) REVERT: B 137 LEU cc_start: 0.9363 (mm) cc_final: 0.8934 (pp) REVERT: B 259 MET cc_start: 0.8920 (tpp) cc_final: 0.8529 (tpp) REVERT: B 275 THR cc_start: 0.8888 (m) cc_final: 0.8469 (p) REVERT: B 294 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9052 (mm) REVERT: B 302 GLU cc_start: 0.8633 (tp30) cc_final: 0.8158 (tp30) REVERT: B 314 GLU cc_start: 0.8026 (mp0) cc_final: 0.7815 (mp0) REVERT: B 399 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8982 (mm) REVERT: B 490 MET cc_start: 0.7963 (mmm) cc_final: 0.7706 (mmm) REVERT: B 547 ASP cc_start: 0.8197 (m-30) cc_final: 0.7800 (t0) REVERT: B 590 GLU cc_start: 0.8728 (tp30) cc_final: 0.8470 (tp30) REVERT: B 641 GLN cc_start: 0.8565 (tt0) cc_final: 0.8165 (tp40) REVERT: C 64 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8868 (tt) REVERT: C 283 ASP cc_start: 0.7608 (t0) cc_final: 0.6936 (t0) REVERT: C 473 MET cc_start: 0.8835 (ttt) cc_final: 0.7656 (ptp) REVERT: C 586 HIS cc_start: 0.7668 (t70) cc_final: 0.7341 (t-170) REVERT: C 589 ASP cc_start: 0.8631 (m-30) cc_final: 0.8266 (p0) REVERT: D 118 GLN cc_start: 0.8248 (tt0) cc_final: 0.7960 (tt0) REVERT: D 308 ASP cc_start: 0.8419 (m-30) cc_final: 0.8060 (m-30) REVERT: D 322 ARG cc_start: 0.8853 (mtm180) cc_final: 0.8345 (tpt170) REVERT: D 391 SER cc_start: 0.9317 (t) cc_final: 0.8900 (p) REVERT: D 441 MET cc_start: 0.9189 (tpp) cc_final: 0.8573 (mtt) REVERT: D 576 MET cc_start: 0.8686 (ttm) cc_final: 0.8400 (ttt) REVERT: D 602 MET cc_start: 0.8136 (ppp) cc_final: 0.7874 (ppp) REVERT: E 123 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8183 (mp0) outliers start: 98 outliers final: 55 residues processed: 340 average time/residue: 0.3328 time to fit residues: 176.5418 Evaluate side-chains 321 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 257 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 622 TYR Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 263 LYS Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 126 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 252 optimal weight: 0.0000 chunk 158 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 122 HIS D 266 GLN D 360 ASN E 42 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21570 Z= 0.207 Angle : 0.684 16.217 29262 Z= 0.332 Chirality : 0.042 0.195 3321 Planarity : 0.003 0.044 3721 Dihedral : 5.409 46.810 2886 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.40 % Favored : 89.37 % Rotamer: Outliers : 3.82 % Allowed : 17.82 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.17), residues: 2625 helix: 0.26 (0.14), residues: 1455 sheet: -1.13 (0.57), residues: 85 loop : -2.95 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 697 HIS 0.004 0.001 HIS B 157 PHE 0.024 0.001 PHE C 433 TYR 0.012 0.001 TYR B 162 ARG 0.008 0.000 ARG E 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 281 time to evaluate : 2.440 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: A 39 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9162 (tm) REVERT: A 99 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8235 (mmm) REVERT: A 275 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8868 (p) REVERT: A 308 ASP cc_start: 0.8744 (m-30) cc_final: 0.8479 (t0) REVERT: A 344 MET cc_start: 0.7944 (mtt) cc_final: 0.7727 (mmt) REVERT: A 382 ASP cc_start: 0.8884 (OUTLIER) cc_final: 0.8634 (p0) REVERT: A 500 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8760 (tt) REVERT: A 569 MET cc_start: 0.8999 (mmt) cc_final: 0.8765 (mmt) REVERT: A 590 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7552 (mm-30) REVERT: A 595 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8348 (mm-40) REVERT: A 627 ARG cc_start: 0.7283 (mmm-85) cc_final: 0.7025 (mmm-85) REVERT: B 96 MET cc_start: 0.8806 (tmm) cc_final: 0.8507 (tmm) REVERT: B 110 MET cc_start: 0.8750 (mtp) cc_final: 0.8470 (mtp) REVERT: B 137 LEU cc_start: 0.9304 (mm) cc_final: 0.8882 (pp) REVERT: B 259 MET cc_start: 0.8908 (tpp) cc_final: 0.8475 (tpp) REVERT: B 275 THR cc_start: 0.8828 (m) cc_final: 0.8445 (p) REVERT: B 294 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8945 (mm) REVERT: B 302 GLU cc_start: 0.8570 (tp30) cc_final: 0.8022 (tp30) REVERT: B 399 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8967 (mm) REVERT: B 490 MET cc_start: 0.7923 (mmm) cc_final: 0.7681 (mmm) REVERT: B 547 ASP cc_start: 0.8187 (m-30) cc_final: 0.7870 (t0) REVERT: B 590 GLU cc_start: 0.8802 (tp30) cc_final: 0.8317 (tp30) REVERT: B 641 GLN cc_start: 0.8522 (tt0) cc_final: 0.8134 (tp40) REVERT: C 64 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8868 (tt) REVERT: C 283 ASP cc_start: 0.7730 (t0) cc_final: 0.7138 (t0) REVERT: C 414 PHE cc_start: 0.8110 (m-10) cc_final: 0.7868 (m-10) REVERT: C 473 MET cc_start: 0.8820 (ttt) cc_final: 0.7752 (ptp) REVERT: C 589 ASP cc_start: 0.8583 (m-30) cc_final: 0.8288 (p0) REVERT: D 78 MET cc_start: 0.8528 (mpt) cc_final: 0.7893 (mpt) REVERT: D 308 ASP cc_start: 0.8436 (m-30) cc_final: 0.8076 (m-30) REVERT: D 391 SER cc_start: 0.9290 (t) cc_final: 0.8818 (p) REVERT: D 441 MET cc_start: 0.9117 (tpp) cc_final: 0.8562 (mtt) REVERT: D 472 GLN cc_start: 0.5636 (OUTLIER) cc_final: 0.5034 (pm20) REVERT: D 576 MET cc_start: 0.8681 (ttm) cc_final: 0.8332 (ttt) REVERT: D 602 MET cc_start: 0.8201 (ppp) cc_final: 0.7930 (ppp) REVERT: E 123 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8116 (mp0) outliers start: 87 outliers final: 47 residues processed: 345 average time/residue: 0.3191 time to fit residues: 172.0454 Evaluate side-chains 318 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 261 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 622 TYR Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 126 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 150 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 160 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 198 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 GLN C 463 ASN ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 HIS ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21570 Z= 0.265 Angle : 0.721 17.383 29262 Z= 0.350 Chirality : 0.043 0.205 3321 Planarity : 0.004 0.045 3721 Dihedral : 5.466 47.394 2886 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.01 % Favored : 88.76 % Rotamer: Outliers : 3.51 % Allowed : 18.57 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.17), residues: 2625 helix: 0.28 (0.14), residues: 1471 sheet: -1.08 (0.57), residues: 84 loop : -2.99 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 697 HIS 0.004 0.001 HIS C 586 PHE 0.020 0.002 PHE A 67 TYR 0.013 0.001 TYR B 525 ARG 0.008 0.000 ARG E 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 267 time to evaluate : 2.278 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: A 39 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9163 (tm) REVERT: A 275 THR cc_start: 0.9124 (m) cc_final: 0.8860 (p) REVERT: A 301 ARG cc_start: 0.8096 (tpt-90) cc_final: 0.7799 (mmm160) REVERT: A 308 ASP cc_start: 0.8751 (m-30) cc_final: 0.8550 (t0) REVERT: A 344 MET cc_start: 0.7971 (mtt) cc_final: 0.7768 (mmt) REVERT: A 382 ASP cc_start: 0.8935 (OUTLIER) cc_final: 0.8642 (p0) REVERT: A 500 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8772 (tt) REVERT: A 501 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8357 (mm) REVERT: A 590 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7552 (mm-30) REVERT: A 595 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8370 (mm-40) REVERT: B 96 MET cc_start: 0.8845 (tmm) cc_final: 0.8562 (tmm) REVERT: B 110 MET cc_start: 0.8754 (mtp) cc_final: 0.8467 (mtp) REVERT: B 137 LEU cc_start: 0.9249 (mm) cc_final: 0.8854 (pp) REVERT: B 259 MET cc_start: 0.8848 (tpp) cc_final: 0.8425 (tpp) REVERT: B 294 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8957 (mm) REVERT: B 302 GLU cc_start: 0.8594 (tp30) cc_final: 0.8022 (tp30) REVERT: B 399 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8959 (mm) REVERT: B 490 MET cc_start: 0.8019 (mmm) cc_final: 0.7723 (mmm) REVERT: B 547 ASP cc_start: 0.8190 (m-30) cc_final: 0.7808 (t0) REVERT: B 590 GLU cc_start: 0.8826 (tp30) cc_final: 0.8322 (tp30) REVERT: B 641 GLN cc_start: 0.8533 (tt0) cc_final: 0.8131 (tp40) REVERT: C 64 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8923 (tt) REVERT: C 283 ASP cc_start: 0.7686 (t0) cc_final: 0.7094 (t0) REVERT: C 473 MET cc_start: 0.8847 (ttt) cc_final: 0.7745 (ptp) REVERT: C 586 HIS cc_start: 0.7768 (t-90) cc_final: 0.7292 (t-170) REVERT: C 589 ASP cc_start: 0.8619 (m-30) cc_final: 0.8236 (p0) REVERT: D 78 MET cc_start: 0.8520 (mpt) cc_final: 0.7862 (mpt) REVERT: D 91 ASN cc_start: 0.7899 (m110) cc_final: 0.7508 (m110) REVERT: D 99 MET cc_start: 0.9091 (mtm) cc_final: 0.8530 (mtm) REVERT: D 308 ASP cc_start: 0.8488 (m-30) cc_final: 0.8122 (m-30) REVERT: D 391 SER cc_start: 0.9297 (t) cc_final: 0.8794 (p) REVERT: D 602 MET cc_start: 0.8196 (ppp) cc_final: 0.7923 (ppp) REVERT: E 72 MET cc_start: 0.8393 (mmt) cc_final: 0.8174 (mmm) outliers start: 80 outliers final: 52 residues processed: 327 average time/residue: 0.3130 time to fit residues: 160.8660 Evaluate side-chains 320 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 261 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 622 TYR Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 444 THR Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 344 MET Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 146 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 0.5980 chunk 241 optimal weight: 1.9990 chunk 220 optimal weight: 7.9990 chunk 235 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 184 optimal weight: 20.0000 chunk 72 optimal weight: 0.4980 chunk 212 optimal weight: 4.9990 chunk 222 optimal weight: 7.9990 chunk 234 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 GLN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21570 Z= 0.183 Angle : 0.698 18.213 29262 Z= 0.333 Chirality : 0.042 0.211 3321 Planarity : 0.003 0.043 3721 Dihedral : 5.249 46.760 2886 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.17 % Favored : 89.60 % Rotamer: Outliers : 2.99 % Allowed : 19.18 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2625 helix: 0.42 (0.14), residues: 1479 sheet: -1.04 (0.57), residues: 84 loop : -2.91 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 697 HIS 0.005 0.001 HIS D 264 PHE 0.028 0.001 PHE C 433 TYR 0.012 0.001 TYR B 338 ARG 0.011 0.000 ARG E 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 286 time to evaluate : 2.313 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: A 39 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9175 (tm) REVERT: A 275 THR cc_start: 0.9087 (m) cc_final: 0.8877 (p) REVERT: A 301 ARG cc_start: 0.8061 (tpt-90) cc_final: 0.7813 (mmm160) REVERT: A 308 ASP cc_start: 0.8724 (m-30) cc_final: 0.8505 (t0) REVERT: A 344 MET cc_start: 0.7845 (mtt) cc_final: 0.7595 (mmt) REVERT: A 382 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8614 (p0) REVERT: A 500 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8718 (tt) REVERT: A 501 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8379 (mm) REVERT: A 569 MET cc_start: 0.8967 (mmt) cc_final: 0.8739 (mmt) REVERT: A 590 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7428 (mm-30) REVERT: A 595 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8298 (mm110) REVERT: B 96 MET cc_start: 0.8810 (tmm) cc_final: 0.8547 (tmm) REVERT: B 110 MET cc_start: 0.8741 (mtp) cc_final: 0.8405 (mtp) REVERT: B 137 LEU cc_start: 0.9200 (mm) cc_final: 0.8815 (pp) REVERT: B 259 MET cc_start: 0.8832 (tpp) cc_final: 0.8404 (tpp) REVERT: B 275 THR cc_start: 0.8789 (m) cc_final: 0.8438 (p) REVERT: B 294 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8891 (mm) REVERT: B 302 GLU cc_start: 0.8492 (tp30) cc_final: 0.7491 (tp30) REVERT: B 399 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8959 (mm) REVERT: B 434 MET cc_start: 0.9012 (mmt) cc_final: 0.8233 (mmm) REVERT: B 490 MET cc_start: 0.7869 (mmm) cc_final: 0.7617 (mmm) REVERT: B 547 ASP cc_start: 0.8155 (m-30) cc_final: 0.7851 (t0) REVERT: B 590 GLU cc_start: 0.8817 (tp30) cc_final: 0.8311 (tp30) REVERT: B 641 GLN cc_start: 0.8432 (tt0) cc_final: 0.8109 (tp40) REVERT: C 64 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8919 (tt) REVERT: C 283 ASP cc_start: 0.7550 (t0) cc_final: 0.6973 (t0) REVERT: C 473 MET cc_start: 0.8807 (ttt) cc_final: 0.7773 (ptp) REVERT: C 586 HIS cc_start: 0.7495 (t-90) cc_final: 0.7171 (t-170) REVERT: C 589 ASP cc_start: 0.8520 (m-30) cc_final: 0.8192 (p0) REVERT: D 40 GLN cc_start: 0.9025 (tt0) cc_final: 0.8211 (tt0) REVERT: D 78 MET cc_start: 0.8510 (mpt) cc_final: 0.7887 (mpt) REVERT: D 80 GLU cc_start: 0.9213 (pm20) cc_final: 0.8602 (pm20) REVERT: D 99 MET cc_start: 0.9053 (mtm) cc_final: 0.8803 (mtm) REVERT: D 278 ASP cc_start: 0.6892 (t0) cc_final: 0.6687 (t0) REVERT: D 308 ASP cc_start: 0.8527 (m-30) cc_final: 0.8176 (m-30) REVERT: D 391 SER cc_start: 0.9247 (t) cc_final: 0.8742 (p) REVERT: D 472 GLN cc_start: 0.5876 (OUTLIER) cc_final: 0.5167 (pm20) REVERT: D 576 MET cc_start: 0.8605 (ttm) cc_final: 0.8277 (ttt) REVERT: D 602 MET cc_start: 0.8215 (ppp) cc_final: 0.7924 (ppp) REVERT: E 109 MET cc_start: 0.9024 (tmm) cc_final: 0.8811 (tmm) REVERT: E 125 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8774 (mm) outliers start: 68 outliers final: 46 residues processed: 334 average time/residue: 0.3218 time to fit residues: 170.5495 Evaluate side-chains 328 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 273 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 622 TYR Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 386 VAL Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 146 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 4.9990 chunk 248 optimal weight: 8.9990 chunk 151 optimal weight: 0.0040 chunk 118 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 261 optimal weight: 0.0020 chunk 240 optimal weight: 0.6980 chunk 207 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 127 optimal weight: 0.3980 overall best weight: 0.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 581 HIS ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 GLN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 21570 Z= 0.157 Angle : 0.705 19.247 29262 Z= 0.333 Chirality : 0.042 0.297 3321 Planarity : 0.003 0.051 3721 Dihedral : 5.103 46.963 2886 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.83 % Favored : 89.90 % Rotamer: Outliers : 2.15 % Allowed : 20.41 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.17), residues: 2625 helix: 0.49 (0.14), residues: 1482 sheet: -0.85 (0.58), residues: 86 loop : -2.84 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 697 HIS 0.004 0.000 HIS B 157 PHE 0.021 0.001 PHE E 16 TYR 0.012 0.001 TYR C 466 ARG 0.009 0.000 ARG E 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 301 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9176 (tm) REVERT: A 275 THR cc_start: 0.9009 (m) cc_final: 0.8689 (p) REVERT: A 301 ARG cc_start: 0.8025 (tpt-90) cc_final: 0.7773 (mmm160) REVERT: A 382 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8573 (p0) REVERT: A 500 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8737 (tt) REVERT: A 569 MET cc_start: 0.8879 (mmt) cc_final: 0.8665 (mmt) REVERT: A 590 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7420 (mm-30) REVERT: A 595 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8252 (mm110) REVERT: B 96 MET cc_start: 0.8736 (tmm) cc_final: 0.8496 (tmm) REVERT: B 110 MET cc_start: 0.8765 (mtp) cc_final: 0.8328 (mtp) REVERT: B 137 LEU cc_start: 0.9146 (mm) cc_final: 0.8765 (pp) REVERT: B 259 MET cc_start: 0.8833 (tpp) cc_final: 0.8418 (tpp) REVERT: B 275 THR cc_start: 0.8803 (m) cc_final: 0.8488 (p) REVERT: B 294 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8805 (mm) REVERT: B 302 GLU cc_start: 0.8417 (tp30) cc_final: 0.7613 (tp30) REVERT: B 399 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8956 (mm) REVERT: B 434 MET cc_start: 0.8984 (mmt) cc_final: 0.8249 (mmm) REVERT: B 547 ASP cc_start: 0.8193 (m-30) cc_final: 0.7861 (t0) REVERT: B 590 GLU cc_start: 0.8735 (tp30) cc_final: 0.8224 (tp30) REVERT: B 641 GLN cc_start: 0.8401 (tt0) cc_final: 0.8067 (tp40) REVERT: C 64 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8904 (tt) REVERT: C 283 ASP cc_start: 0.7413 (t0) cc_final: 0.7021 (t0) REVERT: C 473 MET cc_start: 0.8804 (ttt) cc_final: 0.7817 (ptp) REVERT: C 569 MET cc_start: 0.8910 (mmm) cc_final: 0.8562 (mmm) REVERT: C 586 HIS cc_start: 0.7511 (t-90) cc_final: 0.7169 (t-170) REVERT: C 589 ASP cc_start: 0.8442 (m-30) cc_final: 0.8107 (p0) REVERT: D 40 GLN cc_start: 0.8996 (tt0) cc_final: 0.8286 (tt0) REVERT: D 78 MET cc_start: 0.8494 (mpt) cc_final: 0.7941 (mpt) REVERT: D 80 GLU cc_start: 0.8854 (pm20) cc_final: 0.8449 (pm20) REVERT: D 99 MET cc_start: 0.9070 (mtm) cc_final: 0.8857 (mtm) REVERT: D 259 MET cc_start: 0.9185 (tpp) cc_final: 0.8775 (tpp) REVERT: D 308 ASP cc_start: 0.8396 (m-30) cc_final: 0.8076 (m-30) REVERT: D 391 SER cc_start: 0.9205 (t) cc_final: 0.8708 (p) REVERT: D 441 MET cc_start: 0.8958 (tpp) cc_final: 0.8751 (ttm) REVERT: D 472 GLN cc_start: 0.5870 (OUTLIER) cc_final: 0.5356 (pm20) REVERT: D 576 MET cc_start: 0.8494 (ttm) cc_final: 0.8194 (ttt) REVERT: D 602 MET cc_start: 0.8229 (ppp) cc_final: 0.7935 (ppp) outliers start: 49 outliers final: 26 residues processed: 338 average time/residue: 0.2944 time to fit residues: 158.1240 Evaluate side-chains 301 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 268 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain C residue 29 TRP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 472 GLN Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 622 TYR Chi-restraints excluded: chain E residue 123 GLU Chi-restraints excluded: chain E residue 146 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 10.0000 chunk 221 optimal weight: 0.8980 chunk 63 optimal weight: 0.0270 chunk 191 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 213 optimal weight: 0.5980 chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 HIS ** C 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 HIS D 266 GLN ** D 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.117396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.096293 restraints weight = 51649.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.099315 restraints weight = 24018.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.101313 restraints weight = 14548.998| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21570 Z= 0.161 Angle : 0.700 16.874 29262 Z= 0.331 Chirality : 0.042 0.191 3321 Planarity : 0.003 0.045 3721 Dihedral : 4.987 47.030 2886 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.71 % Favored : 90.06 % Rotamer: Outliers : 1.84 % Allowed : 21.38 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.17), residues: 2625 helix: 0.60 (0.14), residues: 1468 sheet: -0.86 (0.57), residues: 86 loop : -2.77 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 697 HIS 0.002 0.000 HIS B 157 PHE 0.028 0.001 PHE C 433 TYR 0.011 0.001 TYR B 338 ARG 0.011 0.000 ARG D 469 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4267.33 seconds wall clock time: 78 minutes 45.79 seconds (4725.79 seconds total)