Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 08:16:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1n_0593/04_2023/6o1n_0593.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1n_0593/04_2023/6o1n_0593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1n_0593/04_2023/6o1n_0593.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1n_0593/04_2023/6o1n_0593.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1n_0593/04_2023/6o1n_0593.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1n_0593/04_2023/6o1n_0593.pdb" } resolution = 2.9 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= 0.003 sd= 0.074 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 140 5.16 5 C 12660 2.51 5 N 3320 2.21 5 O 3488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 154": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D ARG 355": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 19608 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4902 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 24, 'TRANS': 587} Chain: "B" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4902 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 24, 'TRANS': 587} Chain: "C" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4902 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 24, 'TRANS': 587} Chain: "D" Number of atoms: 4902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4902 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 24, 'TRANS': 587} Time building chain proxies: 10.52, per 1000 atoms: 0.54 Number of scatterers: 19608 At special positions: 0 Unit cell: (134.493, 132.375, 124.962, 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 140 16.00 O 3488 8.00 N 3320 7.00 C 12660 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: 6.90 Conformation dependent library (CDL) restraints added in 3.1 seconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4624 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 4 sheets defined 55.6% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.649A pdb=" N ASP A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 36 " --> pdb=" O TYR A 32 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.594A pdb=" N ALA A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 55 " --> pdb=" O GLN 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: 3.608A pdb=" N VAL A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.613A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.064A pdb=" N VAL A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.547A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A 126 " --> pdb=" O HIS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.536A pdb=" N VAL A 133 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.578A pdb=" N VAL A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.515A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 205' Processing helix chain 'A' and resid 208 through 211 removed outlier: 3.802A pdb=" N PHE A 211 " --> pdb=" O ASN A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 212 through 222 removed outlier: 3.883A pdb=" N LEU A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.548A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.645A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.929A pdb=" N GLN A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.814A pdb=" N VAL A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.564A pdb=" N ALA A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 307 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.643A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.633A pdb=" N MET A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 406 through 411 removed outlier: 4.139A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 443 removed outlier: 3.616A pdb=" N ALA A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.504A pdb=" N LEU A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 removed outlier: 4.275A pdb=" N MET A 466 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 removed outlier: 3.829A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 504 through 512 removed outlier: 3.509A pdb=" N HIS A 509 " --> pdb=" O ALA A 505 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.874A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 4.024A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 581 removed outlier: 3.562A pdb=" N PHE A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 608 removed outlier: 3.803A pdb=" N ARG A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 606 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS A 607 " --> pdb=" O MET A 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 47 removed outlier: 3.649A pdb=" N ASP B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.594A pdb=" N ALA B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 55 " --> pdb=" O GLN B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 64 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.608A pdb=" N VAL B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.612A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 4.064A pdb=" N VAL B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.548A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET B 126 " --> pdb=" O HIS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.536A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.578A pdb=" N VAL B 173 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.515A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 205' Processing helix chain 'B' and resid 208 through 211 removed outlier: 3.802A pdb=" N PHE B 211 " --> pdb=" O ASN B 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 211' Processing helix chain 'B' and resid 212 through 222 removed outlier: 3.882A pdb=" N LEU B 218 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.548A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.646A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 removed outlier: 3.928A pdb=" N GLN B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 262 No H-bonds generated for 'chain 'B' and resid 260 through 262' Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.814A pdb=" N VAL B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.564A pdb=" N ALA B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE B 307 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.643A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 removed outlier: 3.634A pdb=" N MET B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 389 through 394 Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 406 through 411 removed outlier: 4.139A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 443 removed outlier: 3.616A pdb=" N ALA B 433 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.504A pdb=" N LEU B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 removed outlier: 4.276A pdb=" N MET B 466 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 488 removed outlier: 3.829A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.510A pdb=" N HIS B 509 " --> pdb=" O ALA B 505 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.874A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 4.024A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 581 removed outlier: 3.561A pdb=" N PHE B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 608 removed outlier: 3.803A pdb=" N ARG B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 606 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.649A pdb=" N ASP C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 36 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET C 38 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.594A pdb=" N ALA C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU C 55 " --> pdb=" O GLN C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.608A pdb=" N VAL C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.613A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.064A pdb=" N VAL C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.548A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET C 126 " --> pdb=" O HIS C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.536A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.578A pdb=" N VAL C 173 " --> pdb=" O PHE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.515A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 205' Processing helix chain 'C' and resid 208 through 211 removed outlier: 3.801A pdb=" N PHE C 211 " --> pdb=" O ASN C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 211' Processing helix chain 'C' and resid 212 through 222 removed outlier: 3.881A pdb=" N LEU C 218 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 220 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.548A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.645A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 removed outlier: 3.929A pdb=" N GLN C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 262 No H-bonds generated for 'chain 'C' and resid 260 through 262' Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.813A pdb=" N VAL C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 310 removed outlier: 3.565A pdb=" N ALA C 304 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 307 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 327 through 332 removed outlier: 3.644A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 344 removed outlier: 3.633A pdb=" N MET C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 397 through 402 Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 406 through 411 removed outlier: 4.139A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 443 removed outlier: 3.615A pdb=" N ALA C 433 " --> pdb=" O ILE C 429 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 462 removed outlier: 3.503A pdb=" N LEU C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP C 462 " --> pdb=" O LEU C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 469 removed outlier: 4.274A pdb=" N MET C 466 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 488 removed outlier: 3.829A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 504 Processing helix chain 'C' and resid 504 through 512 removed outlier: 3.510A pdb=" N HIS C 509 " --> pdb=" O ALA C 505 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.874A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR C 533 " --> pdb=" O ALA C 529 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 4.023A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 581 removed outlier: 3.562A pdb=" N PHE C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 576 " --> pdb=" O ASN C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 608 removed outlier: 3.803A pdb=" N ARG C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 47 removed outlier: 3.648A pdb=" N ASP D 34 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 36 " --> pdb=" O TYR D 32 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET D 38 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.595A pdb=" N ALA D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU D 55 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 64 Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.609A pdb=" N VAL D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR D 89 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.613A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 4.065A pdb=" N VAL D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.547A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET D 126 " --> pdb=" O HIS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.536A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.578A pdb=" N VAL D 173 " --> pdb=" O PHE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.515A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.538A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 205' Processing helix chain 'D' and resid 208 through 211 removed outlier: 3.802A pdb=" N PHE D 211 " --> pdb=" O ASN D 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 208 through 211' Processing helix chain 'D' and resid 212 through 222 removed outlier: 3.883A pdb=" N LEU D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU D 220 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.548A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.646A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL D 249 " --> pdb=" O LYS D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 removed outlier: 3.928A pdb=" N GLN D 257 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 262 No H-bonds generated for 'chain 'D' and resid 260 through 262' Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.814A pdb=" N VAL D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 310 removed outlier: 3.564A pdb=" N ALA D 304 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 307 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 324 Processing helix chain 'D' and resid 327 through 332 removed outlier: 3.643A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 removed outlier: 3.634A pdb=" N MET D 340 " --> pdb=" O TYR D 336 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 389 through 394 Processing helix chain 'D' and resid 397 through 402 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 406 through 411 removed outlier: 4.140A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 443 removed outlier: 3.616A pdb=" N ALA D 433 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU D 435 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 462 removed outlier: 3.504A pdb=" N LEU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP D 462 " --> pdb=" O LEU D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 469 removed outlier: 4.276A pdb=" N MET D 466 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 488 removed outlier: 3.829A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 504 Processing helix chain 'D' and resid 504 through 512 removed outlier: 3.510A pdb=" N HIS D 509 " --> pdb=" O ALA D 505 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR D 511 " --> pdb=" O ALA D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.874A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR D 533 " --> pdb=" O ALA D 529 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 4.023A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 581 removed outlier: 3.561A pdb=" N PHE D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 576 " --> pdb=" O ASN D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 608 removed outlier: 3.803A pdb=" N ARG D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 606 " --> pdb=" O VAL D 602 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS D 607 " --> pdb=" O MET D 603 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 268 removed outlier: 6.832A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A 274 " --> pdb=" O ASN A 635 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 264 through 268 removed outlier: 6.831A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR B 274 " --> pdb=" O ASN B 635 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 264 through 268 removed outlier: 6.831A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C 274 " --> pdb=" O ASN C 635 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 264 through 268 removed outlier: 6.832A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR D 274 " --> pdb=" O ASN D 635 " (cutoff:3.500A) 536 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.37 Time building geometry restraints manager: 7.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3164 1.31 - 1.44: 5472 1.44 - 1.56: 11197 1.56 - 1.68: 3 1.68 - 1.81: 228 Bond restraints: 20064 Sorted by residual: bond pdb=" N TYR D 623 " pdb=" CA TYR D 623 " ideal model delta sigma weight residual 1.462 1.557 -0.096 1.44e-02 4.82e+03 4.40e+01 bond pdb=" N TYR B 623 " pdb=" CA TYR B 623 " ideal model delta sigma weight residual 1.462 1.557 -0.095 1.44e-02 4.82e+03 4.39e+01 bond pdb=" N TYR C 623 " pdb=" CA TYR C 623 " ideal model delta sigma weight residual 1.462 1.557 -0.095 1.44e-02 4.82e+03 4.36e+01 bond pdb=" N TYR A 623 " pdb=" CA TYR A 623 " ideal model delta sigma weight residual 1.462 1.557 -0.095 1.44e-02 4.82e+03 4.36e+01 bond pdb=" N PRO C 614 " pdb=" CD PRO C 614 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.17e+01 ... (remaining 20059 not shown) Histogram of bond angle deviations from ideal: 94.65 - 102.78: 150 102.78 - 110.91: 7203 110.91 - 119.05: 9163 119.05 - 127.18: 10460 127.18 - 135.31: 272 Bond angle restraints: 27248 Sorted by residual: angle pdb=" N GLN C 370 " pdb=" CA GLN C 370 " pdb=" C GLN C 370 " ideal model delta sigma weight residual 110.30 126.53 -16.23 1.50e+00 4.44e-01 1.17e+02 angle pdb=" N GLN A 370 " pdb=" CA GLN A 370 " pdb=" C GLN A 370 " ideal model delta sigma weight residual 110.30 126.53 -16.23 1.50e+00 4.44e-01 1.17e+02 angle pdb=" N GLN B 370 " pdb=" CA GLN B 370 " pdb=" C GLN B 370 " ideal model delta sigma weight residual 110.30 126.51 -16.21 1.50e+00 4.44e-01 1.17e+02 angle pdb=" N GLN D 370 " pdb=" CA GLN D 370 " pdb=" C GLN D 370 " ideal model delta sigma weight residual 110.30 126.49 -16.19 1.50e+00 4.44e-01 1.16e+02 angle pdb=" N LEU C 229 " pdb=" CA LEU C 229 " pdb=" C LEU C 229 " ideal model delta sigma weight residual 110.24 94.65 15.59 1.47e+00 4.63e-01 1.12e+02 ... (remaining 27243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 11047 15.19 - 30.37: 719 30.37 - 45.56: 126 45.56 - 60.74: 36 60.74 - 75.93: 8 Dihedral angle restraints: 11936 sinusoidal: 4780 harmonic: 7156 Sorted by residual: dihedral pdb=" C PHE B 611 " pdb=" N PHE B 611 " pdb=" CA PHE B 611 " pdb=" CB PHE B 611 " ideal model delta harmonic sigma weight residual -122.60 -102.25 -20.35 0 2.50e+00 1.60e-01 6.63e+01 dihedral pdb=" C PHE D 611 " pdb=" N PHE D 611 " pdb=" CA PHE D 611 " pdb=" CB PHE D 611 " ideal model delta harmonic sigma weight residual -122.60 -102.26 -20.34 0 2.50e+00 1.60e-01 6.62e+01 dihedral pdb=" C PHE A 611 " pdb=" N PHE A 611 " pdb=" CA PHE A 611 " pdb=" CB PHE A 611 " ideal model delta harmonic sigma weight residual -122.60 -102.26 -20.34 0 2.50e+00 1.60e-01 6.62e+01 ... (remaining 11933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2639 0.090 - 0.181: 405 0.181 - 0.271: 32 0.271 - 0.361: 18 0.361 - 0.452: 6 Chirality restraints: 3100 Sorted by residual: chirality pdb=" CA PHE C 611 " pdb=" N PHE C 611 " pdb=" C PHE C 611 " pdb=" CB PHE C 611 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CA PHE D 611 " pdb=" N PHE D 611 " pdb=" C PHE D 611 " pdb=" CB PHE D 611 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" CA PHE B 611 " pdb=" N PHE B 611 " pdb=" C PHE B 611 " pdb=" CB PHE B 611 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.06e+00 ... (remaining 3097 not shown) Planarity restraints: 3460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 623 " -0.023 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C TYR B 623 " 0.085 2.00e-02 2.50e+03 pdb=" O TYR B 623 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY B 624 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 623 " -0.023 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C TYR A 623 " 0.085 2.00e-02 2.50e+03 pdb=" O TYR A 623 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY A 624 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 623 " -0.023 2.00e-02 2.50e+03 4.89e-02 2.39e+01 pdb=" C TYR C 623 " 0.084 2.00e-02 2.50e+03 pdb=" O TYR C 623 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY C 624 " -0.027 2.00e-02 2.50e+03 ... (remaining 3457 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 52 2.47 - 3.07: 11599 3.07 - 3.68: 27979 3.68 - 4.29: 40943 4.29 - 4.90: 66731 Nonbonded interactions: 147304 Sorted by model distance: nonbonded pdb=" O GLN B 230 " pdb=" O SER B 231 " model vdw 1.856 3.040 nonbonded pdb=" O GLN A 230 " pdb=" O SER A 231 " model vdw 1.857 3.040 nonbonded pdb=" O GLN C 230 " pdb=" O SER C 231 " model vdw 1.857 3.040 nonbonded pdb=" O GLN D 230 " pdb=" O SER D 231 " model vdw 1.857 3.040 nonbonded pdb=" O HIS D 228 " pdb=" C LEU D 229 " model vdw 2.009 3.270 ... (remaining 147299 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 'B' selection = chain 'C' selection = chain 'D' } 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 individual isotropic 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.450 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 53.550 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: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 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 : 0.011 0.119 20064 Z= 0.685 Angle : 1.374 16.229 27248 Z= 0.811 Chirality : 0.072 0.452 3100 Planarity : 0.009 0.097 3460 Dihedral : 11.022 75.928 7312 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.39 % Favored : 93.11 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.52 % 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: -6.01 (0.12), residues: 2440 helix: -4.73 (0.05), residues: 1272 sheet: -3.48 (0.46), residues: 84 loop : -2.88 (0.16), residues: 1084 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 552 time to evaluate : 2.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 567 average time/residue: 1.2950 time to fit residues: 826.0617 Evaluate side-chains 300 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 285 time to evaluate : 2.238 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 8 residues processed: 10 average time/residue: 0.4429 time to fit residues: 9.1255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 63 optimal weight: 0.0050 chunk 124 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 191 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 74 GLN A 127 ASN A 128 GLN A 157 HIS A 208 ASN A 217 ASN A 228 HIS A 238 HIS A 252 ASN A 446 ASN A 483 GLN A 519 ASN A 572 ASN A 596 GLN B 51 GLN B 127 ASN B 128 GLN B 157 HIS B 238 HIS B 252 ASN B 446 ASN B 483 GLN C 51 GLN C 128 GLN C 157 HIS C 228 HIS C 238 HIS C 252 ASN C 446 ASN D 51 GLN D 214 GLN D 238 HIS D 446 ASN D 519 ASN D 572 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 20064 Z= 0.197 Angle : 0.714 12.031 27248 Z= 0.362 Chirality : 0.042 0.229 3100 Planarity : 0.005 0.047 3460 Dihedral : 6.196 27.396 2672 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.86 % Favored : 93.98 % Rotamer Outliers : 4.29 % 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: -4.79 (0.14), residues: 2440 helix: -3.41 (0.10), residues: 1276 sheet: -3.31 (0.46), residues: 84 loop : -2.72 (0.17), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 356 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 18 residues processed: 409 average time/residue: 1.2062 time to fit residues: 562.1210 Evaluate side-chains 280 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 262 time to evaluate : 2.053 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 4 average time/residue: 0.4680 time to fit residues: 5.3621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 239 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 220 optimal weight: 0.2980 chunk 75 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 157 HIS A 206 GLN B 74 GLN B 128 GLN B 157 HIS B 252 ASN C 74 GLN C 127 ASN C 128 GLN C 157 HIS C 252 ASN C 267 GLN C 483 GLN C 518 ASN D 127 ASN D 214 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 20064 Z= 0.226 Angle : 0.678 12.538 27248 Z= 0.338 Chirality : 0.043 0.256 3100 Planarity : 0.004 0.044 3460 Dihedral : 5.572 25.367 2672 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.19 % Favored : 93.77 % Rotamer Outliers : 4.10 % 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: -3.87 (0.15), residues: 2440 helix: -2.50 (0.12), residues: 1284 sheet: -2.91 (0.51), residues: 76 loop : -2.50 (0.18), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 319 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 31 residues processed: 382 average time/residue: 1.1357 time to fit residues: 498.6777 Evaluate side-chains 301 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 270 time to evaluate : 2.383 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 24 residues processed: 7 average time/residue: 0.4249 time to fit residues: 7.4023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 222 optimal weight: 0.5980 chunk 235 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 211 optimal weight: 0.0770 chunk 63 optimal weight: 4.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 310 GLN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 206 GLN B 587 GLN C 157 HIS C 206 GLN C 217 ASN C 267 GLN C 310 GLN D 582 HIS D 636 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 20064 Z= 0.180 Angle : 0.640 13.720 27248 Z= 0.313 Chirality : 0.041 0.199 3100 Planarity : 0.004 0.039 3460 Dihedral : 5.174 22.723 2672 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 4.34 % 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: -3.47 (0.15), residues: 2440 helix: -2.01 (0.13), residues: 1316 sheet: -3.04 (0.50), residues: 76 loop : -2.53 (0.18), residues: 1048 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 291 time to evaluate : 2.426 Fit side-chains revert: symmetry clash outliers start: 92 outliers final: 29 residues processed: 353 average time/residue: 1.0912 time to fit residues: 446.1263 Evaluate side-chains 297 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 268 time to evaluate : 2.248 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 22 residues processed: 8 average time/residue: 0.4042 time to fit residues: 7.6707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 0.0670 chunk 133 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 201 optimal weight: 0.2980 chunk 163 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 211 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 519 ASN B 157 HIS B 587 GLN C 157 HIS D 129 ASN D 582 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 20064 Z= 0.160 Angle : 0.631 14.438 27248 Z= 0.304 Chirality : 0.041 0.289 3100 Planarity : 0.004 0.041 3460 Dihedral : 4.887 21.163 2672 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 4.01 % 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: -3.02 (0.16), residues: 2440 helix: -1.58 (0.13), residues: 1332 sheet: -3.44 (0.45), residues: 84 loop : -2.33 (0.18), residues: 1024 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 295 time to evaluate : 2.456 Fit side-chains revert: symmetry clash outliers start: 85 outliers final: 30 residues processed: 345 average time/residue: 1.0847 time to fit residues: 433.4818 Evaluate side-chains 296 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 266 time to evaluate : 2.331 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 23 residues processed: 9 average time/residue: 0.4781 time to fit residues: 8.9729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 138 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 195 optimal weight: 0.0050 chunk 109 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS B 157 HIS B 587 GLN C 157 HIS D 74 GLN D 582 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 20064 Z= 0.180 Angle : 0.634 14.164 27248 Z= 0.307 Chirality : 0.041 0.231 3100 Planarity : 0.004 0.041 3460 Dihedral : 4.830 22.431 2672 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 3.92 % 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: -2.51 (0.16), residues: 2440 helix: -1.17 (0.14), residues: 1284 sheet: -3.12 (0.48), residues: 76 loop : -2.09 (0.18), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 283 time to evaluate : 2.153 Fit side-chains revert: symmetry clash outliers start: 83 outliers final: 27 residues processed: 336 average time/residue: 1.0888 time to fit residues: 424.5877 Evaluate side-chains 296 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 269 time to evaluate : 2.254 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 6 average time/residue: 0.6114 time to fit residues: 7.8170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 172 optimal weight: 0.9980 chunk 133 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 235 optimal weight: 0.4980 chunk 147 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 252 ASN B 157 HIS B 572 ASN B 582 HIS B 587 GLN C 157 HIS D 582 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 20064 Z= 0.264 Angle : 0.699 12.727 27248 Z= 0.341 Chirality : 0.044 0.233 3100 Planarity : 0.004 0.048 3460 Dihedral : 5.119 23.018 2672 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer Outliers : 3.44 % 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: -2.55 (0.16), residues: 2440 helix: -1.23 (0.14), residues: 1292 sheet: -2.96 (0.52), residues: 76 loop : -2.09 (0.18), residues: 1072 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 284 time to evaluate : 2.350 Fit side-chains outliers start: 73 outliers final: 26 residues processed: 334 average time/residue: 1.0640 time to fit residues: 411.8126 Evaluate side-chains 292 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 266 time to evaluate : 2.241 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 7 average time/residue: 0.5273 time to fit residues: 7.8978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 0.0470 chunk 45 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 160 optimal weight: 0.2980 chunk 116 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 184 optimal weight: 2.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 158 ASN B 51 GLN B 157 HIS C 157 HIS C 587 GLN D 157 HIS D 310 GLN D 572 ASN D 582 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.6519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 20064 Z= 0.161 Angle : 0.667 13.455 27248 Z= 0.321 Chirality : 0.041 0.193 3100 Planarity : 0.004 0.049 3460 Dihedral : 4.774 22.110 2672 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 2.17 % 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: -2.13 (0.17), residues: 2440 helix: -0.85 (0.14), residues: 1292 sheet: -2.93 (0.50), residues: 76 loop : -1.93 (0.19), residues: 1072 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 299 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 20 residues processed: 329 average time/residue: 1.0364 time to fit residues: 396.7481 Evaluate side-chains 282 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 262 time to evaluate : 2.293 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 17 residues processed: 3 average time/residue: 0.4132 time to fit residues: 4.8753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.2980 chunk 225 optimal weight: 0.0370 chunk 205 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 131 optimal weight: 0.0370 chunk 95 optimal weight: 2.9990 chunk 172 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 207 optimal weight: 0.6980 chunk 218 optimal weight: 10.0000 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 587 GLN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS B 158 ASN B 572 ASN C 157 HIS C 587 GLN D 157 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.6700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 20064 Z= 0.159 Angle : 0.667 14.873 27248 Z= 0.317 Chirality : 0.041 0.203 3100 Planarity : 0.003 0.037 3460 Dihedral : 4.594 21.615 2672 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 1.70 % 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: -1.88 (0.17), residues: 2440 helix: -0.53 (0.15), residues: 1288 sheet: -3.24 (0.46), residues: 84 loop : -1.93 (0.19), residues: 1068 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 281 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 21 residues processed: 302 average time/residue: 1.0311 time to fit residues: 363.4005 Evaluate side-chains 288 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 267 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 4 average time/residue: 0.3096 time to fit residues: 5.0961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 0.9980 chunk 231 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 161 optimal weight: 0.0670 chunk 243 optimal weight: 0.4980 chunk 223 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 157 HIS ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 HIS C 157 HIS C 582 HIS C 587 GLN D 157 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.6796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 20064 Z= 0.176 Angle : 0.678 15.352 27248 Z= 0.320 Chirality : 0.041 0.179 3100 Planarity : 0.004 0.056 3460 Dihedral : 4.555 25.342 2672 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer Outliers : 1.93 % 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: -1.73 (0.17), residues: 2440 helix: -0.38 (0.15), residues: 1292 sheet: -3.17 (0.46), residues: 84 loop : -1.90 (0.19), residues: 1064 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 280 time to evaluate : 2.296 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 20 residues processed: 307 average time/residue: 1.0796 time to fit residues: 383.9301 Evaluate side-chains 279 residues out of total 2120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 259 time to evaluate : 2.271 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 18 residues processed: 3 average time/residue: 0.6716 time to fit residues: 5.6601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 178 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 193 optimal weight: 0.0060 chunk 81 optimal weight: 8.9990 chunk 199 optimal weight: 7.9990 chunk 24 optimal weight: 0.1980 chunk 35 optimal weight: 0.3980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 157 HIS B 238 HIS B 473 GLN C 157 HIS D 157 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.177552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.124982 restraints weight = 25474.994| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 3.02 r_work: 0.3520 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.6947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 20064 Z= 0.162 Angle : 0.669 14.893 27248 Z= 0.315 Chirality : 0.040 0.172 3100 Planarity : 0.004 0.060 3460 Dihedral : 4.422 22.004 2672 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer Outliers : 1.42 % 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: -1.53 (0.17), residues: 2440 helix: -0.23 (0.15), residues: 1300 sheet: -3.14 (0.45), residues: 84 loop : -1.79 (0.19), residues: 1056 =============================================================================== Job complete usr+sys time: 7366.23 seconds wall clock time: 131 minutes 11.13 seconds (7871.13 seconds total)