Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 09:26:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2g_8962/07_2023/6e2g_8962.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2g_8962/07_2023/6e2g_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_8962/07_2023/6e2g_8962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2g_8962/07_2023/6e2g_8962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2g_8962/07_2023/6e2g_8962.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6e2g_8962/07_2023/6e2g_8962.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-5013/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: 10.38, per 1000 atoms: 0.49 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: 8.26 Conformation dependent library (CDL) restraints added in 3.0 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: 0.86 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: 5.68 Time building geometry restraints manager: 8.91 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.110 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 50.040 Find NCS groups from input model: 1.430 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.780 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.471 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 outliers start: 24 outliers final: 7 residues processed: 516 average time/residue: 0.3615 time to fit residues: 278.4498 Evaluate side-chains 290 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 283 time to evaluate : 2.652 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2143 time to fit residues: 6.6997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 67 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 205 optimal weight: 5.9990 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: 1.6984 ------------------------------------------------------------------------------- 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 237 ASN A 251 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN A 369 GLN 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 251 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 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 Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 21570 Z= 0.228 Angle : 0.776 16.777 29262 Z= 0.390 Chirality : 0.044 0.198 3321 Planarity : 0.005 0.051 3721 Dihedral : 6.515 40.609 2881 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.25 % Favored : 89.56 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 1452 sheet: -1.63 (0.57), residues: 83 loop : -3.23 (0.18), residues: 1090 *********************** 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 423 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 358 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 27 residues processed: 408 average time/residue: 0.3175 time to fit residues: 203.5336 Evaluate side-chains 292 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 265 time to evaluate : 2.480 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2113 time to fit residues: 13.8983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 65 optimal weight: 0.4980 chunk 238 optimal weight: 0.9990 chunk 257 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 191 optimal weight: 0.5980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** 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 251 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 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 HIS D 266 GLN E 8 GLN E 135 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 21570 Z= 0.211 Angle : 0.727 16.170 29262 Z= 0.357 Chirality : 0.043 0.198 3321 Planarity : 0.004 0.044 3721 Dihedral : 5.934 39.998 2881 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.78 % Favored : 88.99 % Rotamer Outliers : 2.41 % 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: -2.99 (0.15), residues: 2625 helix: -1.20 (0.13), residues: 1453 sheet: -1.23 (0.58), residues: 81 loop : -3.12 (0.18), residues: 1091 *********************** 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 362 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 307 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 22 residues processed: 347 average time/residue: 0.3128 time to fit residues: 173.1225 Evaluate side-chains 288 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 266 time to evaluate : 2.558 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2240 time to fit residues: 12.5067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 123 optimal weight: 20.0000 chunk 26 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 239 optimal weight: 0.0070 chunk 253 optimal weight: 20.0000 chunk 124 optimal weight: 0.7980 chunk 226 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 overall best weight: 1.5202 ------------------------------------------------------------------------------- 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 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 HIS A 581 HIS B 31 GLN ** 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 251 ASN ** 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 74 GLN D 369 GLN D 512 GLN E 137 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 21570 Z= 0.190 Angle : 0.696 14.560 29262 Z= 0.341 Chirality : 0.042 0.171 3321 Planarity : 0.003 0.039 3721 Dihedral : 5.545 38.636 2881 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.98 % Favored : 89.79 % Rotamer Outliers : 2.28 % 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: -2.41 (0.16), residues: 2625 helix: -0.63 (0.13), residues: 1468 sheet: -1.20 (0.58), residues: 83 loop : -3.05 (0.18), residues: 1074 *********************** 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 354 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 302 time to evaluate : 2.367 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 outliers start: 52 outliers final: 13 residues processed: 345 average time/residue: 0.3076 time to fit residues: 168.9472 Evaluate side-chains 277 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 264 time to evaluate : 2.457 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2036 time to fit residues: 8.0101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 4.9990 chunk 143 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 175 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 chunk 227 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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** ** B 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 21570 Z= 0.213 Angle : 0.685 15.633 29262 Z= 0.336 Chirality : 0.042 0.172 3321 Planarity : 0.003 0.038 3721 Dihedral : 5.375 37.602 2881 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.59 % Favored : 89.30 % Rotamer Outliers : 2.24 % 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: -2.03 (0.16), residues: 2625 helix: -0.28 (0.14), residues: 1473 sheet: -0.97 (0.60), residues: 79 loop : -2.96 (0.19), residues: 1073 *********************** 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 324 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 273 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 23 residues processed: 310 average time/residue: 0.3444 time to fit residues: 164.1676 Evaluate side-chains 275 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 252 time to evaluate : 2.466 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1901 time to fit residues: 11.5099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 6.9990 chunk 228 optimal weight: 0.0570 chunk 50 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 253 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- 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 289 GLN C 425 HIS C 463 ASN ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 HIS D 266 GLN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 21570 Z= 0.173 Angle : 0.672 15.686 29262 Z= 0.327 Chirality : 0.042 0.217 3321 Planarity : 0.003 0.038 3721 Dihedral : 5.180 35.944 2881 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.68 % Favored : 90.13 % Rotamer Outliers : 1.40 % 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: -1.79 (0.17), residues: 2625 helix: -0.02 (0.14), residues: 1466 sheet: -1.03 (0.58), residues: 83 loop : -2.93 (0.19), residues: 1076 *********************** 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 315 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 283 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 11 residues processed: 307 average time/residue: 0.3249 time to fit residues: 157.0972 Evaluate side-chains 262 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 251 time to evaluate : 2.653 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2157 time to fit residues: 7.8309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 185 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 252 optimal weight: 20.0000 chunk 158 optimal weight: 0.2980 chunk 153 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- 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 512 GLN ** 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 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 HIS ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 21570 Z= 0.255 Angle : 0.722 16.061 29262 Z= 0.348 Chirality : 0.043 0.291 3321 Planarity : 0.003 0.035 3721 Dihedral : 5.208 34.438 2881 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.74 % Favored : 89.14 % Rotamer Outliers : 1.10 % 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: -1.68 (0.17), residues: 2625 helix: 0.09 (0.14), residues: 1470 sheet: -1.02 (0.59), residues: 83 loop : -2.92 (0.19), residues: 1072 *********************** 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 278 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 253 time to evaluate : 2.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 267 average time/residue: 0.3464 time to fit residues: 145.8563 Evaluate side-chains 252 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 241 time to evaluate : 2.780 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2474 time to fit residues: 8.9724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 172 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 23 optimal weight: 8.9990 chunk 198 optimal weight: 0.2980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 GLN ** C 482 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS ** D 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4586 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= 0.181 Angle : 0.699 15.452 29262 Z= 0.332 Chirality : 0.042 0.200 3321 Planarity : 0.003 0.037 3721 Dihedral : 5.071 33.374 2881 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.79 % Favored : 90.06 % Rotamer Outliers : 1.27 % 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: -1.50 (0.17), residues: 2625 helix: 0.26 (0.14), residues: 1467 sheet: -1.09 (0.57), residues: 83 loop : -2.87 (0.19), residues: 1075 *********************** 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 290 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 261 time to evaluate : 2.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 10 residues processed: 280 average time/residue: 0.3297 time to fit residues: 146.5792 Evaluate side-chains 255 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 245 time to evaluate : 2.435 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2091 time to fit residues: 6.9986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 0.8980 chunk 241 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 235 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 184 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 212 optimal weight: 0.7980 chunk 222 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 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 122 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 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 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 21570 Z= 0.190 Angle : 0.705 15.478 29262 Z= 0.335 Chirality : 0.042 0.206 3321 Planarity : 0.003 0.033 3721 Dihedral : 5.015 32.485 2881 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.10 % Favored : 89.79 % Rotamer Outliers : 0.53 % 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: -1.40 (0.17), residues: 2625 helix: 0.33 (0.14), residues: 1472 sheet: -1.01 (0.58), residues: 82 loop : -2.80 (0.19), residues: 1071 *********************** 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 276 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 264 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 3 residues processed: 270 average time/residue: 0.3648 time to fit residues: 154.7659 Evaluate side-chains 261 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 258 time to evaluate : 2.499 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2098 time to fit residues: 4.4731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 240 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 8 GLN E 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 21570 Z= 0.176 Angle : 0.710 14.974 29262 Z= 0.337 Chirality : 0.042 0.185 3321 Planarity : 0.003 0.052 3721 Dihedral : 4.944 31.686 2881 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.87 % Favored : 90.02 % Rotamer Outliers : 0.26 % 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: -1.28 (0.17), residues: 2625 helix: 0.45 (0.14), residues: 1460 sheet: -1.04 (0.57), residues: 84 loop : -2.76 (0.19), residues: 1081 ********************** 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 280 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 274 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 275 average time/residue: 0.3315 time to fit residues: 145.1157 Evaluate side-chains 251 residues out of total 2278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 2.384 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2251 time to fit residues: 3.5018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 0.8980 chunk 221 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 191 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 213 optimal weight: 0.0020 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 B 639 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 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.118683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.096237 restraints weight = 52690.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.099331 restraints weight = 25296.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.101363 restraints weight = 15733.165| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 21570 Z= 0.166 Angle : 0.708 14.631 29262 Z= 0.334 Chirality : 0.041 0.186 3321 Planarity : 0.003 0.056 3721 Dihedral : 4.827 30.825 2881 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.56 % Favored : 90.32 % Rotamer Outliers : 0.31 % 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: -1.23 (0.17), residues: 2625 helix: 0.49 (0.14), residues: 1467 sheet: -0.91 (0.57), residues: 84 loop : -2.76 (0.19), residues: 1074 =============================================================================== Job complete usr+sys time: 3965.45 seconds wall clock time: 73 minutes 7.87 seconds (4387.87 seconds total)