Starting phenix.real_space_refine on Mon Mar 18 18:15:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1d_30041/03_2024/6m1d_30041.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1d_30041/03_2024/6m1d_30041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1d_30041/03_2024/6m1d_30041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1d_30041/03_2024/6m1d_30041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1d_30041/03_2024/6m1d_30041.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1d_30041/03_2024/6m1d_30041.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 14154 2.51 5 N 3524 2.21 5 O 3970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 25": "OE1" <-> "OE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A GLU 437": "OE1" <-> "OE2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B GLU 182": "OE1" <-> "OE2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B GLU 433": "OE1" <-> "OE2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "B ARG 518": "NH1" <-> "NH2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "B TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 671": "NH1" <-> "NH2" Residue "B ARG 678": "NH1" <-> "NH2" Residue "B GLU 699": "OE1" <-> "OE2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "B ARG 768": "NH1" <-> "NH2" Residue "C GLU 25": "OE1" <-> "OE2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C GLU 394": "OE1" <-> "OE2" Residue "C GLU 437": "OE1" <-> "OE2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 501": "OE1" <-> "OE2" Residue "C ARG 607": "NH1" <-> "NH2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 433": "OE1" <-> "OE2" Residue "D GLU 489": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 564": "OE1" <-> "OE2" Residue "D TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 671": "NH1" <-> "NH2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "D GLU 699": "OE1" <-> "OE2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "D ARG 768": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21776 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} Chain: "B" Number of atoms: 6089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6089 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 35, 'TRANS': 712} Chain: "C" Number of atoms: 4799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4799 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 31, 'TRANS': 573} Chain: "D" Number of atoms: 6089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 748, 6089 Classifications: {'peptide': 748} Link IDs: {'PTRANS': 35, 'TRANS': 712} Time building chain proxies: 11.41, per 1000 atoms: 0.52 Number of scatterers: 21776 At special positions: 0 Unit cell: (109.787, 130.44, 184.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 3970 8.00 N 3524 7.00 C 14154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 383 " distance=2.02 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.04 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 383 " distance=2.02 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.83 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 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: 9.25 Conformation dependent library (CDL) restraints added in 3.9 seconds 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5080 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 10 sheets defined 58.5% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 38 through 50 removed outlier: 3.888A pdb=" N MET A 42 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS A 45 " --> pdb=" O TYR A 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 46 " --> pdb=" O MET A 42 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS A 49 " --> pdb=" O CYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 removed outlier: 4.097A pdb=" N GLN A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 97 removed outlier: 3.806A pdb=" N PHE A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU A 77 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix removed outlier: 3.885A pdb=" N TYR A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.738A pdb=" N TRP A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 142 removed outlier: 4.590A pdb=" N MET A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 169 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.663A pdb=" N PHE A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N TRP A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.688A pdb=" N ALA A 204 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER A 206 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 207 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 209 " --> pdb=" O TRP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 222 removed outlier: 3.646A pdb=" N THR A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 244 removed outlier: 3.525A pdb=" N VAL A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 236 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.672A pdb=" N LEU A 262 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 4.019A pdb=" N TRP A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.691A pdb=" N SER A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 348 removed outlier: 3.767A pdb=" N SER A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N CYS A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 337 " --> pdb=" O TYR A 333 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 371 Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.548A pdb=" N PHE A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.869A pdb=" N ALA A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 431 removed outlier: 3.530A pdb=" N VAL A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 422 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N MET A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.615A pdb=" N VAL A 440 " --> pdb=" O MET A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 464 removed outlier: 3.593A pdb=" N CYS A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 475 removed outlier: 3.597A pdb=" N PHE A 471 " --> pdb=" O LEU A 468 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 472 " --> pdb=" O ILE A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 removed outlier: 3.678A pdb=" N TRP A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 485 " --> pdb=" O TRP A 481 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER A 487 " --> pdb=" O SER A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 508 removed outlier: 4.414A pdb=" N ILE A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE A 497 " --> pdb=" O PRO A 493 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 503 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 504 " --> pdb=" O CYS A 500 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 522 removed outlier: 3.691A pdb=" N ASP A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU A 519 " --> pdb=" O ASN A 515 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 536 removed outlier: 4.078A pdb=" N GLN A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP A 534 " --> pdb=" O TRP A 530 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG A 535 " --> pdb=" O GLN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.729A pdb=" N MET A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A 543 " --> pdb=" O PRO A 539 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 546 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 608 removed outlier: 4.109A pdb=" N ALA A 590 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Proline residue: A 593 - end of helix removed outlier: 4.136A pdb=" N THR A 596 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 4.871A pdb=" N ALA A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 32 Processing helix chain 'B' and resid 36 through 49 removed outlier: 4.423A pdb=" N SER B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 77 removed outlier: 4.557A pdb=" N ALA B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TRP B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 129 removed outlier: 3.992A pdb=" N ILE B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR B 127 " --> pdb=" O MET B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 148 through 154 Processing helix chain 'B' and resid 157 through 170 removed outlier: 3.775A pdb=" N ARG B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 180 through 194 removed outlier: 3.539A pdb=" N LYS B 187 " --> pdb=" O TYR B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 removed outlier: 3.654A pdb=" N ARG B 204 " --> pdb=" O GLY B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 208 Processing helix chain 'B' and resid 229 through 252 removed outlier: 3.506A pdb=" N ILE B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) Proline residue: B 235 - end of helix removed outlier: 3.743A pdb=" N MET B 249 " --> pdb=" O ARG B 245 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 305 through 317 removed outlier: 4.031A pdb=" N LYS B 313 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER B 317 " --> pdb=" O LYS B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 383 removed outlier: 4.270A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N HIS B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS B 378 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR B 381 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 407 Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 434 through 447 removed outlier: 4.085A pdb=" N LEU B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU B 440 " --> pdb=" O ILE B 436 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 441 " --> pdb=" O ASN B 437 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 465 removed outlier: 3.579A pdb=" N TYR B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 456 " --> pdb=" O PHE B 452 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU B 457 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.709A pdb=" N TRP B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 479 " --> pdb=" O LYS B 475 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET B 480 " --> pdb=" O LYS B 476 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 481 " --> pdb=" O TRP B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.852A pdb=" N SER B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 521 removed outlier: 3.939A pdb=" N THR B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 518 " --> pdb=" O ARG B 514 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 521 " --> pdb=" O THR B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 530 removed outlier: 3.597A pdb=" N GLN B 526 " --> pdb=" O GLN B 522 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU B 527 " --> pdb=" O PHE B 523 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA B 528 " --> pdb=" O GLN B 524 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS B 530 " --> pdb=" O GLN B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 533 No H-bonds generated for 'chain 'B' and resid 531 through 533' Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.572A pdb=" N GLN B 552 " --> pdb=" O THR B 548 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN B 556 " --> pdb=" O GLN B 552 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 575 removed outlier: 3.903A pdb=" N VAL B 573 " --> pdb=" O ALA B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 593 removed outlier: 3.695A pdb=" N THR B 593 " --> pdb=" O GLU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 613 through 617 Processing helix chain 'B' and resid 636 through 658 removed outlier: 3.654A pdb=" N SER B 645 " --> pdb=" O TYR B 641 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET B 651 " --> pdb=" O VAL B 647 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 656 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.670A pdb=" N VAL B 700 " --> pdb=" O PRO B 696 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS B 702 " --> pdb=" O THR B 698 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER B 707 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 712 removed outlier: 3.872A pdb=" N ILE B 711 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN B 712 " --> pdb=" O ARG B 708 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 707 through 712' Processing helix chain 'B' and resid 741 through 767 removed outlier: 3.621A pdb=" N VAL B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 749 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY B 751 " --> pdb=" O GLY B 747 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 753 " --> pdb=" O VAL B 749 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL B 754 " --> pdb=" O MET B 750 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL B 755 " --> pdb=" O GLY B 751 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY B 756 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE B 757 " --> pdb=" O ILE B 753 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL B 758 " --> pdb=" O VAL B 754 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 760 " --> pdb=" O GLY B 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.890A pdb=" N MET C 42 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS C 45 " --> pdb=" O TYR C 41 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 46 " --> pdb=" O MET C 42 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS C 49 " --> pdb=" O CYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 removed outlier: 4.098A pdb=" N GLN C 63 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 97 removed outlier: 3.807A pdb=" N PHE C 74 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE C 76 " --> pdb=" O ILE C 72 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU C 77 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU C 78 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE C 83 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix removed outlier: 3.884A pdb=" N TYR C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY C 93 " --> pdb=" O GLU C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 107 removed outlier: 3.739A pdb=" N TRP C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 142 removed outlier: 4.590A pdb=" N MET C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN C 130 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 169 Processing helix chain 'C' and resid 170 through 179 removed outlier: 3.650A pdb=" N PHE C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TRP C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 212 removed outlier: 3.688A pdb=" N ALA C 204 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP C 205 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER C 206 " --> pdb=" O ALA C 202 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 207 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR C 209 " --> pdb=" O TRP C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 222 removed outlier: 3.646A pdb=" N THR C 219 " --> pdb=" O GLY C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 244 removed outlier: 5.156A pdb=" N LEU C 234 " --> pdb=" O PRO C 230 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE C 236 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 239 " --> pdb=" O THR C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 removed outlier: 3.672A pdb=" N LEU C 262 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 279 removed outlier: 4.018A pdb=" N TRP C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 290 removed outlier: 3.691A pdb=" N SER C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 348 removed outlier: 3.767A pdb=" N SER C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 309 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN C 310 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 314 " --> pdb=" O ASN C 310 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 320 " --> pdb=" O TYR C 316 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 321 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N CYS C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE C 337 " --> pdb=" O TYR C 333 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 371 Processing helix chain 'C' and resid 373 through 377 Processing helix chain 'C' and resid 396 through 401 removed outlier: 3.548A pdb=" N PHE C 400 " --> pdb=" O THR C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 408 removed outlier: 3.869A pdb=" N ALA C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 431 removed outlier: 3.530A pdb=" N VAL C 418 " --> pdb=" O PRO C 414 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE C 421 " --> pdb=" O SER C 417 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 422 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N MET C 423 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.615A pdb=" N VAL C 440 " --> pdb=" O MET C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 464 removed outlier: 3.593A pdb=" N CYS C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 475 removed outlier: 3.596A pdb=" N PHE C 471 " --> pdb=" O LEU C 468 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 472 " --> pdb=" O ILE C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 488 removed outlier: 3.677A pdb=" N TRP C 481 " --> pdb=" O SER C 477 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 484 " --> pdb=" O TYR C 480 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C 485 " --> pdb=" O TRP C 481 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 508 removed outlier: 4.414A pdb=" N ILE C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE C 497 " --> pdb=" O PRO C 493 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 498 " --> pdb=" O LEU C 494 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU C 501 " --> pdb=" O ILE C 497 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET C 502 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE C 503 " --> pdb=" O PHE C 499 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER C 504 " --> pdb=" O CYS C 500 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 522 removed outlier: 3.691A pdb=" N ASP C 517 " --> pdb=" O ARG C 513 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU C 519 " --> pdb=" O ASN C 515 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE C 520 " --> pdb=" O LYS C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 536 removed outlier: 4.077A pdb=" N GLN C 531 " --> pdb=" O ASN C 527 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP C 534 " --> pdb=" O TRP C 530 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG C 535 " --> pdb=" O GLN C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 552 removed outlier: 3.729A pdb=" N MET C 542 " --> pdb=" O SER C 538 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU C 543 " --> pdb=" O PRO C 539 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 546 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE C 550 " --> pdb=" O PHE C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 608 removed outlier: 4.110A pdb=" N ALA C 590 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Proline residue: C 593 - end of helix removed outlier: 4.136A pdb=" N THR C 596 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE C 597 " --> pdb=" O PRO C 593 " (cutoff:3.500A) Proline residue: C 598 - end of helix removed outlier: 4.870A pdb=" N ALA C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 32 Processing helix chain 'D' and resid 36 through 49 removed outlier: 4.423A pdb=" N SER D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 63 through 77 removed outlier: 4.096A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.691A pdb=" N LEU D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 129 removed outlier: 3.993A pdb=" N ILE D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR D 122 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 148 through 154 Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.776A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 180 through 194 removed outlier: 3.539A pdb=" N LYS D 187 " --> pdb=" O TYR D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.654A pdb=" N ARG D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 208 Processing helix chain 'D' and resid 229 through 252 removed outlier: 3.506A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.744A pdb=" N MET D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 305 through 317 removed outlier: 4.030A pdb=" N LYS D 313 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL D 316 " --> pdb=" O GLU D 312 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER D 317 " --> pdb=" O LYS D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 383 removed outlier: 4.269A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N HIS D 374 " --> pdb=" O LEU D 370 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN D 380 " --> pdb=" O MET D 376 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 407 removed outlier: 3.567A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 413 Processing helix chain 'D' and resid 434 through 447 removed outlier: 4.084A pdb=" N LEU D 439 " --> pdb=" O GLU D 435 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU D 440 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 removed outlier: 3.580A pdb=" N TYR D 454 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 456 " --> pdb=" O PHE D 452 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU D 457 " --> pdb=" O THR D 453 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.709A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET D 480 " --> pdb=" O LYS D 476 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS D 481 " --> pdb=" O TRP D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.852A pdb=" N SER D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 530 removed outlier: 4.101A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU D 527 " --> pdb=" O PHE D 523 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA D 528 " --> pdb=" O GLN D 524 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS D 530 " --> pdb=" O GLN D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 533 No H-bonds generated for 'chain 'D' and resid 531 through 533' Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.572A pdb=" N GLN D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN D 556 " --> pdb=" O GLN D 552 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 572 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.694A pdb=" N THR D 593 " --> pdb=" O GLU D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 597 Processing helix chain 'D' and resid 613 through 617 Processing helix chain 'D' and resid 636 through 658 removed outlier: 3.654A pdb=" N SER D 645 " --> pdb=" O TYR D 641 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET D 651 " --> pdb=" O VAL D 647 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 656 " --> pdb=" O ARG D 652 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS D 657 " --> pdb=" O GLN D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 668 No H-bonds generated for 'chain 'D' and resid 666 through 668' Processing helix chain 'D' and resid 696 through 707 removed outlier: 3.671A pdb=" N VAL D 700 " --> pdb=" O PRO D 696 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYS D 702 " --> pdb=" O THR D 698 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER D 707 " --> pdb=" O ALA D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 712 removed outlier: 3.873A pdb=" N ILE D 711 " --> pdb=" O SER D 707 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN D 712 " --> pdb=" O ARG D 708 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 707 through 712' Processing helix chain 'D' and resid 741 through 767 removed outlier: 3.621A pdb=" N VAL D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL D 749 " --> pdb=" O VAL D 745 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY D 751 " --> pdb=" O GLY D 747 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE D 753 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL D 754 " --> pdb=" O MET D 750 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL D 755 " --> pdb=" O GLY D 751 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY D 756 " --> pdb=" O VAL D 752 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ILE D 757 " --> pdb=" O ILE D 753 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL D 758 " --> pdb=" O VAL D 754 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU D 760 " --> pdb=" O GLY D 756 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 560 through 562 Processing sheet with id=AA2, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA3, first strand: chain 'B' and resid 262 through 263 removed outlier: 5.650A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AA5, first strand: chain 'B' and resid 618 through 621 removed outlier: 6.841A pdb=" N SER B 680 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU B 675 " --> pdb=" O SER B 680 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 560 through 562 Processing sheet with id=AA7, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AA8, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.650A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 347 through 348 Processing sheet with id=AB1, first strand: chain 'D' and resid 618 through 620 removed outlier: 6.841A pdb=" N SER D 680 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LEU D 675 " --> pdb=" O SER D 680 " (cutoff:3.500A) 749 hydrogen bonds defined for protein. 2133 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: 6.48 Time building geometry restraints manager: 10.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6741 1.34 - 1.46: 5643 1.46 - 1.58: 9790 1.58 - 1.71: 0 1.71 - 1.83: 210 Bond restraints: 22384 Sorted by residual: bond pdb=" C GLU D 145 " pdb=" N PRO D 146 " ideal model delta sigma weight residual 1.332 1.375 -0.043 8.20e-03 1.49e+04 2.69e+01 bond pdb=" C GLU B 145 " pdb=" N PRO B 146 " ideal model delta sigma weight residual 1.332 1.374 -0.042 8.20e-03 1.49e+04 2.65e+01 bond pdb=" N PRO B 677 " pdb=" CD PRO B 677 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.88e+01 bond pdb=" N PRO B 565 " pdb=" CD PRO B 565 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.84e+01 bond pdb=" N PRO A 147 " pdb=" CD PRO A 147 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.79e+01 ... (remaining 22379 not shown) Histogram of bond angle deviations from ideal: 99.28 - 107.13: 810 107.13 - 114.99: 12849 114.99 - 122.84: 14906 122.84 - 130.69: 1746 130.69 - 138.55: 161 Bond angle restraints: 30472 Sorted by residual: angle pdb=" N ASN D 51 " pdb=" CA ASN D 51 " pdb=" C ASN D 51 " ideal model delta sigma weight residual 113.16 123.29 -10.13 1.24e+00 6.50e-01 6.68e+01 angle pdb=" N LYS B 363 " pdb=" CA LYS B 363 " pdb=" C LYS B 363 " ideal model delta sigma weight residual 113.20 102.67 10.53 1.36e+00 5.41e-01 6.00e+01 angle pdb=" N ILE B 421 " pdb=" CA ILE B 421 " pdb=" C ILE B 421 " ideal model delta sigma weight residual 113.20 106.25 6.95 9.60e-01 1.09e+00 5.24e+01 angle pdb=" N ILE D 421 " pdb=" CA ILE D 421 " pdb=" C ILE D 421 " ideal model delta sigma weight residual 113.20 106.25 6.95 9.60e-01 1.09e+00 5.24e+01 angle pdb=" O GLY D 395 " pdb=" C GLY D 395 " pdb=" N ALA D 396 " ideal model delta sigma weight residual 122.71 127.63 -4.92 7.80e-01 1.64e+00 3.98e+01 ... (remaining 30467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 11274 17.89 - 35.78: 1322 35.78 - 53.67: 365 53.67 - 71.56: 129 71.56 - 89.45: 40 Dihedral angle restraints: 13130 sinusoidal: 5230 harmonic: 7900 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 383 " pdb=" CB CYS A 383 " ideal model delta sinusoidal sigma weight residual -86.00 -161.21 75.21 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 383 " pdb=" CB CYS C 383 " ideal model delta sinusoidal sigma weight residual -86.00 -161.21 75.21 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CA ASN D 432 " pdb=" C ASN D 432 " pdb=" N GLU D 433 " pdb=" CA GLU D 433 " ideal model delta harmonic sigma weight residual -180.00 -150.83 -29.17 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 13127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2840 0.081 - 0.161: 443 0.161 - 0.242: 36 0.242 - 0.323: 8 0.323 - 0.403: 5 Chirality restraints: 3332 Sorted by residual: chirality pdb=" CA ASN D 51 " pdb=" N ASN D 51 " pdb=" C ASN D 51 " pdb=" CB ASN D 51 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA CYS D 344 " pdb=" N CYS D 344 " pdb=" C CYS D 344 " pdb=" CB CYS D 344 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CG LEU B 423 " pdb=" CB LEU B 423 " pdb=" CD1 LEU B 423 " pdb=" CD2 LEU B 423 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 3329 not shown) Planarity restraints: 3870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 649 " 0.028 2.00e-02 2.50e+03 2.70e-02 1.46e+01 pdb=" CG TYR D 649 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR D 649 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR D 649 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR D 649 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR D 649 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 649 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 649 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 649 " -0.028 2.00e-02 2.50e+03 2.68e-02 1.44e+01 pdb=" CG TYR B 649 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR B 649 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 649 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR B 649 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR B 649 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 649 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 649 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 345 " 0.051 5.00e-02 4.00e+02 7.87e-02 9.91e+00 pdb=" N PRO D 346 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO D 346 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 346 " 0.043 5.00e-02 4.00e+02 ... (remaining 3867 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 532 2.61 - 3.19: 19442 3.19 - 3.76: 38615 3.76 - 4.33: 52003 4.33 - 4.90: 77587 Nonbonded interactions: 188179 Sorted by model distance: nonbonded pdb=" O CYS D 361 " pdb=" OG1 THR D 362 " model vdw 2.043 2.440 nonbonded pdb=" O PHE A 144 " pdb=" CG GLN A 145 " model vdw 2.074 3.440 nonbonded pdb=" O THR A 212 " pdb=" OG1 THR A 212 " model vdw 2.165 2.440 nonbonded pdb=" O THR C 212 " pdb=" OG1 THR C 212 " model vdw 2.165 2.440 nonbonded pdb=" O VAL D 343 " pdb=" CB CYS D 344 " model vdw 2.175 3.440 ... (remaining 188174 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' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 6.150 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 57.490 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 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 : 0.005 0.082 22384 Z= 0.335 Angle : 1.198 13.546 30472 Z= 0.707 Chirality : 0.060 0.403 3332 Planarity : 0.008 0.079 3870 Dihedral : 18.157 89.453 8020 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.85 % Allowed : 9.30 % Favored : 89.84 % Rotamer: Outliers : 9.51 % Allowed : 8.21 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -5.09 (0.12), residues: 2698 helix: -3.75 (0.09), residues: 1296 sheet: -2.30 (0.62), residues: 64 loop : -3.01 (0.15), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 635 HIS 0.008 0.002 HIS B 195 PHE 0.028 0.002 PHE D 523 TYR 0.065 0.003 TYR D 649 ARG 0.011 0.001 ARG D 393 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 30 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 CYS cc_start: 0.9520 (OUTLIER) cc_final: 0.9271 (t) REVERT: A 137 MET cc_start: 0.9806 (OUTLIER) cc_final: 0.9504 (ptp) REVERT: A 231 TYR cc_start: 0.8719 (m-80) cc_final: 0.8435 (m-80) REVERT: A 355 VAL cc_start: 0.9533 (OUTLIER) cc_final: 0.9159 (m) REVERT: A 365 GLN cc_start: 0.9553 (OUTLIER) cc_final: 0.9231 (mm110) REVERT: A 436 MET cc_start: 0.9482 (OUTLIER) cc_final: 0.9055 (tmm) outliers start: 39 outliers final: 4 residues processed: 63 average time/residue: 0.1113 time to fit residues: 10.1860 Evaluate side-chains 29 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 20 time to evaluate : 0.546 Evaluate side-chains 154 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 79 time to evaluate : 0.705 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: B 44 SER cc_start: 0.5801 (OUTLIER) cc_final: 0.5215 (p) REVERT: B 64 ASN cc_start: 0.9397 (m-40) cc_final: 0.8996 (m-40) REVERT: B 113 SER cc_start: 0.6761 (OUTLIER) cc_final: 0.6484 (p) REVERT: B 152 MET cc_start: 0.8817 (mmt) cc_final: 0.8468 (mmp) REVERT: B 180 TYR cc_start: 0.9007 (m-10) cc_final: 0.8690 (m-80) REVERT: B 190 MET cc_start: 0.9205 (ttm) cc_final: 0.8866 (tmm) REVERT: B 203 TRP cc_start: 0.9263 (OUTLIER) cc_final: 0.8955 (m-10) REVERT: B 249 MET cc_start: 0.8891 (mmm) cc_final: 0.8533 (tpp) REVERT: B 270 MET cc_start: 0.8934 (tpp) cc_final: 0.8281 (tpp) REVERT: B 462 MET cc_start: 0.9197 (mtm) cc_final: 0.8979 (ttm) REVERT: B 505 HIS cc_start: 0.8541 (m-70) cc_final: 0.8309 (m90) REVERT: B 545 SER cc_start: 0.4614 (OUTLIER) cc_final: 0.4047 (p) REVERT: B 623 SER cc_start: 0.7492 (OUTLIER) cc_final: 0.7223 (p) REVERT: B 655 PHE cc_start: 0.9079 (m-10) cc_final: 0.8647 (m-10) REVERT: B 664 LEU cc_start: 0.8697 (mt) cc_final: 0.8431 (tp) REVERT: B 707 SER cc_start: 0.9195 (OUTLIER) cc_final: 0.7888 (p) REVERT: B 750 MET cc_start: 0.9316 (ptt) cc_final: 0.9057 (ptt) outliers start: 75 outliers final: 16 residues processed: 143 average time/residue: 0.1851 time to fit residues: 34.5226 Evaluate side-chains 70 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 48 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 5.9990 chunk 203 optimal weight: 0.5980 chunk 112 optimal weight: 9.9990 chunk 69 optimal weight: 0.0010 chunk 137 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 chunk 81 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 243 optimal weight: 20.0000 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 130 ASN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN A 357 GLN A 444 GLN A 574 GLN Total number of N/Q/H flips: 6 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 42 GLN ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN B 241 HIS B 300 GLN B 401 HIS B 508 ASN ** B 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 616 GLN B 653 GLN B 660 ASN B 735 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 22384 Z= 0.218 Angle : 0.774 9.828 30472 Z= 0.415 Chirality : 0.047 0.215 3332 Planarity : 0.006 0.063 3870 Dihedral : 7.248 29.523 2914 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.23 % Favored : 90.88 % Rotamer: Outliers : 0.34 % Allowed : 4.61 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -3.98 (0.14), residues: 2698 helix: -2.56 (0.11), residues: 1410 sheet: -1.45 (0.82), residues: 40 loop : -2.72 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 48 HIS 0.002 0.001 HIS D 345 PHE 0.019 0.002 PHE D 315 TYR 0.019 0.002 TYR D 641 ARG 0.010 0.001 ARG B 678 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 129 TYR cc_start: 0.9624 (m-80) cc_final: 0.9196 (m-80) REVERT: A 137 MET cc_start: 0.9807 (mtm) cc_final: 0.9532 (ptp) REVERT: A 231 TYR cc_start: 0.8606 (m-80) cc_final: 0.8306 (m-80) REVERT: A 312 PHE cc_start: 0.9592 (m-80) cc_final: 0.9353 (m-80) REVERT: A 488 TYR cc_start: 0.7938 (t80) cc_final: 0.7448 (t80) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1331 time to fit residues: 5.8345 Evaluate side-chains 22 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.552 Evaluate side-chains 65 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 63 ASN cc_start: 0.9158 (t0) cc_final: 0.8917 (t0) REVERT: B 64 ASN cc_start: 0.9354 (m-40) cc_final: 0.8958 (m-40) REVERT: B 152 MET cc_start: 0.8830 (mmt) cc_final: 0.8595 (mmp) REVERT: B 190 MET cc_start: 0.9219 (ttm) cc_final: 0.8834 (tmm) REVERT: B 270 MET cc_start: 0.8833 (tpp) cc_final: 0.8098 (tpp) REVERT: B 640 MET cc_start: 0.8935 (mmp) cc_final: 0.8652 (mmm) REVERT: B 655 PHE cc_start: 0.8516 (m-10) cc_final: 0.8149 (m-10) REVERT: B 664 LEU cc_start: 0.8644 (mt) cc_final: 0.8243 (tp) REVERT: B 722 LEU cc_start: 0.8804 (mp) cc_final: 0.8590 (mt) outliers start: 4 outliers final: 3 residues processed: 65 average time/residue: 0.1952 time to fit residues: 17.0933 Evaluate side-chains 45 residues out of total 662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.7564 > 50: distance: 0 - 1: 20.618 distance: 0 - 6: 34.117 distance: 1 - 30: 33.678 distance: 2 - 3: 3.891 distance: 6 - 7: 4.758 distance: 7 - 8: 14.786 distance: 7 - 10: 22.911 distance: 8 - 9: 11.398 distance: 8 - 13: 11.259 distance: 10 - 11: 15.093 distance: 10 - 12: 19.190 distance: 13 - 14: 8.331 distance: 14 - 15: 7.989 distance: 14 - 17: 17.259 distance: 15 - 16: 12.208 distance: 15 - 21: 6.951 distance: 17 - 18: 14.663 distance: 18 - 19: 46.576 distance: 18 - 20: 36.908 distance: 21 - 22: 32.834 distance: 22 - 23: 37.189 distance: 22 - 25: 25.419 distance: 23 - 24: 48.272 distance: 23 - 30: 6.719 distance: 25 - 26: 22.732 distance: 26 - 27: 3.026 distance: 30 - 31: 33.248 distance: 31 - 32: 23.179 distance: 32 - 33: 33.527 distance: 32 - 34: 26.432 distance: 34 - 35: 3.965 distance: 35 - 36: 30.115 distance: 35 - 38: 7.403 distance: 36 - 37: 40.553 distance: 36 - 42: 26.327 distance: 38 - 39: 22.020 distance: 38 - 40: 43.228 distance: 39 - 41: 55.756 distance: 42 - 43: 4.650 distance: 42 - 48: 22.315 distance: 43 - 44: 6.355 distance: 43 - 46: 12.689 distance: 44 - 45: 19.189 distance: 44 - 49: 8.599 distance: 45 - 77: 17.080 distance: 46 - 47: 8.642 distance: 47 - 48: 20.553 distance: 49 - 50: 9.076 distance: 50 - 51: 8.307 distance: 50 - 53: 11.548 distance: 51 - 52: 28.766 distance: 51 - 57: 7.336 distance: 53 - 54: 5.688 distance: 54 - 55: 5.339 distance: 54 - 56: 13.744 distance: 57 - 58: 6.492 distance: 58 - 59: 9.832 distance: 58 - 61: 7.063 distance: 59 - 60: 12.056 distance: 59 - 65: 7.270 distance: 61 - 62: 6.928 distance: 62 - 63: 4.631 distance: 62 - 64: 11.957 distance: 65 - 66: 6.322 distance: 66 - 67: 9.438 distance: 66 - 69: 7.419 distance: 67 - 68: 12.644 distance: 67 - 77: 4.995 distance: 69 - 70: 6.224 distance: 70 - 71: 3.594 distance: 70 - 72: 3.262