Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 07:26:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ji1_9832/07_2023/6ji1_9832.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ji1_9832/07_2023/6ji1_9832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ji1_9832/07_2023/6ji1_9832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ji1_9832/07_2023/6ji1_9832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ji1_9832/07_2023/6ji1_9832.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ji1_9832/07_2023/6ji1_9832.pdb" } resolution = 4.1 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= 0.000 sd= 0.004 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 80 5.16 5 C 9284 2.51 5 N 2232 2.21 5 O 2396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "B PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 245": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "C PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 245": "NH1" <-> "NH2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "D PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 304": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 13992 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3498 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 448} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3498 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 448} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3498 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 448} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3498 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 448} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Time building chain proxies: 7.02, per 1000 atoms: 0.50 Number of scatterers: 13992 At special positions: 0 Unit cell: (127.89, 127.89, 77.43, 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 80 16.00 O 2396 8.00 N 2232 7.00 C 9284 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: 5.57 Conformation dependent library (CDL) restraints added in 1.9 seconds 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3368 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 0 sheets defined 73.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 removed outlier: 3.752A pdb=" N MET A 15 " --> pdb=" O THR A 11 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR A 16 " --> pdb=" O HIS A 12 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 42 removed outlier: 3.582A pdb=" N MET A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN A 41 " --> pdb=" O TYR A 37 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 72 removed outlier: 3.970A pdb=" N LEU A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TRP A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE A 61 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Proline residue: A 65 - end of helix removed outlier: 3.736A pdb=" N GLY A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'A' and resid 87 through 95 removed outlier: 3.710A pdb=" N VAL A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.930A pdb=" N LEU A 110 " --> pdb=" O MET A 106 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLY A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 129 removed outlier: 4.257A pdb=" N GLY A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 159 removed outlier: 4.619A pdb=" N ILE A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE A 156 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N MET A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.586A pdb=" N VAL A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN A 169 " --> pdb=" O LYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 198 removed outlier: 3.678A pdb=" N PHE A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N CYS A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS A 186 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 200 No H-bonds generated for 'chain 'A' and resid 199 through 200' Processing helix chain 'A' and resid 201 through 206 removed outlier: 3.576A pdb=" N ALA A 204 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN A 205 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 236 removed outlier: 4.803A pdb=" N ILE A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.879A pdb=" N ARG A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 removed outlier: 3.713A pdb=" N HIS A 261 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 292 removed outlier: 3.657A pdb=" N PHE A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 287 " --> pdb=" O GLN A 283 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 324 through 327 Processing helix chain 'A' and resid 328 through 336 removed outlier: 3.637A pdb=" N ILE A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET A 334 " --> pdb=" O PRO A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 381 removed outlier: 3.628A pdb=" N LEU A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY A 363 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A 364 " --> pdb=" O PHE A 360 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA A 365 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE A 373 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N TYR A 374 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY A 375 " --> pdb=" O PHE A 371 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 378 " --> pdb=" O TYR A 374 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 380 " --> pdb=" O PHE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 403 removed outlier: 3.829A pdb=" N GLY A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A 397 " --> pdb=" O TRP A 393 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 399 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 439 removed outlier: 4.296A pdb=" N TYR A 429 " --> pdb=" O MET A 425 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE A 430 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 459 through 484 removed outlier: 3.820A pdb=" N ASN A 465 " --> pdb=" O PRO A 461 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU A 466 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 467 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA A 481 " --> pdb=" O CYS A 477 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 482 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.936A pdb=" N LEU A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 487 through 492' Processing helix chain 'B' and resid 9 through 32 removed outlier: 3.752A pdb=" N MET B 15 " --> pdb=" O THR B 11 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR B 16 " --> pdb=" O HIS B 12 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL B 17 " --> pdb=" O SER B 13 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE B 20 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR B 29 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.583A pdb=" N MET B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLN B 41 " --> pdb=" O TYR B 37 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 72 removed outlier: 3.970A pdb=" N LEU B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TRP B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 61 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Proline residue: B 65 - end of helix removed outlier: 3.736A pdb=" N GLY B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 Processing helix chain 'B' and resid 87 through 95 removed outlier: 3.711A pdb=" N VAL B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.930A pdb=" N LEU B 110 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY B 111 " --> pdb=" O PHE B 107 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 112 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 129 removed outlier: 4.258A pdb=" N GLY B 125 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN B 126 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU B 127 " --> pdb=" O ASN B 123 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 159 removed outlier: 4.619A pdb=" N ILE B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE B 156 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N MET B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU B 159 " --> pdb=" O THR B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 169 removed outlier: 3.585A pdb=" N VAL B 168 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 198 removed outlier: 3.678A pdb=" N PHE B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N CYS B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS B 186 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 200 No H-bonds generated for 'chain 'B' and resid 199 through 200' Processing helix chain 'B' and resid 201 through 206 removed outlier: 3.575A pdb=" N ALA B 204 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN B 205 " --> pdb=" O SER B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 236 removed outlier: 4.803A pdb=" N ILE B 222 " --> pdb=" O LYS B 218 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.878A pdb=" N ARG B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL B 253 " --> pdb=" O TYR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 removed outlier: 3.713A pdb=" N HIS B 261 " --> pdb=" O ILE B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 292 removed outlier: 3.657A pdb=" N PHE B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 287 " --> pdb=" O GLN B 283 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 302 Processing helix chain 'B' and resid 324 through 327 Processing helix chain 'B' and resid 328 through 336 removed outlier: 3.635A pdb=" N ILE B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET B 334 " --> pdb=" O PRO B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 381 removed outlier: 3.628A pdb=" N LEU B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE B 364 " --> pdb=" O PHE B 360 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA B 365 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE B 373 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR B 374 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY B 375 " --> pdb=" O PHE B 371 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY B 378 " --> pdb=" O TYR B 374 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE B 380 " --> pdb=" O PHE B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.829A pdb=" N GLY B 394 " --> pdb=" O VAL B 390 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA B 396 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER B 397 " --> pdb=" O TRP B 393 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR B 398 " --> pdb=" O GLY B 394 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 399 " --> pdb=" O TYR B 395 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 439 removed outlier: 4.295A pdb=" N TYR B 429 " --> pdb=" O MET B 425 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE B 430 " --> pdb=" O MET B 426 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 445 Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 459 through 484 removed outlier: 3.820A pdb=" N ASN B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU B 466 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 467 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN B 468 " --> pdb=" O THR B 464 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE B 479 " --> pdb=" O VAL B 475 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE B 480 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA B 481 " --> pdb=" O CYS B 477 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 482 " --> pdb=" O THR B 478 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 removed outlier: 3.936A pdb=" N LEU B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 487 through 492' Processing helix chain 'C' and resid 9 through 32 removed outlier: 3.753A pdb=" N MET C 15 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR C 16 " --> pdb=" O HIS C 12 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL C 17 " --> pdb=" O SER C 13 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR C 29 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY C 30 " --> pdb=" O PHE C 26 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 42 removed outlier: 3.582A pdb=" N MET C 39 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLN C 41 " --> pdb=" O TYR C 37 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.970A pdb=" N LEU C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C 53 " --> pdb=" O ARG C 49 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TRP C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA C 59 " --> pdb=" O SER C 55 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE C 61 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Proline residue: C 65 - end of helix removed outlier: 3.736A pdb=" N GLY C 72 " --> pdb=" O GLY C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 85 Processing helix chain 'C' and resid 87 through 95 removed outlier: 3.711A pdb=" N VAL C 91 " --> pdb=" O GLY C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 119 removed outlier: 3.930A pdb=" N LEU C 110 " --> pdb=" O MET C 106 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLY C 111 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 112 " --> pdb=" O SER C 108 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 129 removed outlier: 4.257A pdb=" N GLY C 125 " --> pdb=" O LYS C 121 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN C 126 " --> pdb=" O PRO C 122 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU C 127 " --> pdb=" O ASN C 123 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 159 removed outlier: 4.620A pdb=" N ILE C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE C 156 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N MET C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU C 159 " --> pdb=" O THR C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 removed outlier: 3.586A pdb=" N VAL C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASN C 169 " --> pdb=" O LYS C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 198 removed outlier: 3.677A pdb=" N PHE C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N CYS C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS C 186 " --> pdb=" O PHE C 182 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 200 No H-bonds generated for 'chain 'C' and resid 199 through 200' Processing helix chain 'C' and resid 201 through 206 removed outlier: 3.575A pdb=" N ALA C 204 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASN C 205 " --> pdb=" O SER C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 236 removed outlier: 4.803A pdb=" N ILE C 222 " --> pdb=" O LYS C 218 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.878A pdb=" N ARG C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 253 " --> pdb=" O TYR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 removed outlier: 3.712A pdb=" N HIS C 261 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 292 removed outlier: 3.657A pdb=" N PHE C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 287 " --> pdb=" O GLN C 283 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE C 288 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE C 290 " --> pdb=" O PHE C 286 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR C 291 " --> pdb=" O PHE C 287 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'C' and resid 324 through 327 Processing helix chain 'C' and resid 328 through 336 removed outlier: 3.635A pdb=" N ILE C 333 " --> pdb=" O ASN C 329 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET C 334 " --> pdb=" O PRO C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 372 removed outlier: 3.627A pdb=" N LEU C 362 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY C 363 " --> pdb=" O LYS C 359 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE C 364 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 381 removed outlier: 3.823A pdb=" N GLY C 378 " --> pdb=" O TYR C 374 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE C 380 " --> pdb=" O PHE C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 403 removed outlier: 3.830A pdb=" N GLY C 394 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA C 396 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER C 397 " --> pdb=" O TRP C 393 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR C 398 " --> pdb=" O GLY C 394 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER C 399 " --> pdb=" O TYR C 395 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 439 removed outlier: 4.296A pdb=" N TYR C 429 " --> pdb=" O MET C 425 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE C 430 " --> pdb=" O MET C 426 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA C 432 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 446 through 448 No H-bonds generated for 'chain 'C' and resid 446 through 448' Processing helix chain 'C' and resid 459 through 484 removed outlier: 3.820A pdb=" N ASN C 465 " --> pdb=" O PRO C 461 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU C 466 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE C 467 " --> pdb=" O TYR C 463 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN C 468 " --> pdb=" O THR C 464 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LYS C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE C 480 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA C 481 " --> pdb=" O CYS C 477 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 482 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL C 484 " --> pdb=" O ILE C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 removed outlier: 3.937A pdb=" N LEU C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 487 through 492' Processing helix chain 'D' and resid 9 through 32 removed outlier: 3.752A pdb=" N MET D 15 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR D 16 " --> pdb=" O HIS D 12 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL D 17 " --> pdb=" O SER D 13 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR D 29 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY D 30 " --> pdb=" O PHE D 26 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 42 removed outlier: 3.584A pdb=" N MET D 39 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLN D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG D 42 " --> pdb=" O PHE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 72 removed outlier: 3.970A pdb=" N LEU D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TRP D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE D 61 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Proline residue: D 65 - end of helix removed outlier: 3.736A pdb=" N GLY D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 85 Processing helix chain 'D' and resid 87 through 95 removed outlier: 3.710A pdb=" N VAL D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.930A pdb=" N LEU D 110 " --> pdb=" O MET D 106 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLY D 111 " --> pdb=" O PHE D 107 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL D 112 " --> pdb=" O SER D 108 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY D 116 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 129 removed outlier: 4.257A pdb=" N GLY D 125 " --> pdb=" O LYS D 121 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN D 126 " --> pdb=" O PRO D 122 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU D 127 " --> pdb=" O ASN D 123 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 159 removed outlier: 4.619A pdb=" N ILE D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE D 156 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER D 157 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N MET D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU D 159 " --> pdb=" O THR D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 169 removed outlier: 3.585A pdb=" N VAL D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 198 removed outlier: 3.677A pdb=" N PHE D 182 " --> pdb=" O TRP D 178 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N CYS D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS D 186 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 200 No H-bonds generated for 'chain 'D' and resid 199 through 200' Processing helix chain 'D' and resid 201 through 206 removed outlier: 3.575A pdb=" N ALA D 204 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN D 205 " --> pdb=" O SER D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 236 removed outlier: 4.802A pdb=" N ILE D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 255 removed outlier: 3.879A pdb=" N ARG D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL D 253 " --> pdb=" O TYR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 removed outlier: 3.712A pdb=" N HIS D 261 " --> pdb=" O ILE D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 292 removed outlier: 3.657A pdb=" N PHE D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE D 287 " --> pdb=" O GLN D 283 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE D 290 " --> pdb=" O PHE D 286 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR D 291 " --> pdb=" O PHE D 287 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN D 292 " --> pdb=" O PHE D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 302 Processing helix chain 'D' and resid 324 through 327 Processing helix chain 'D' and resid 328 through 336 removed outlier: 3.636A pdb=" N ILE D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET D 334 " --> pdb=" O PRO D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 381 removed outlier: 3.628A pdb=" N LEU D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY D 363 " --> pdb=" O LYS D 359 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE D 364 " --> pdb=" O PHE D 360 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE D 373 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR D 374 " --> pdb=" O GLY D 370 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY D 375 " --> pdb=" O PHE D 371 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY D 378 " --> pdb=" O TYR D 374 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE D 380 " --> pdb=" O PHE D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 403 removed outlier: 3.829A pdb=" N GLY D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA D 396 " --> pdb=" O ILE D 392 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER D 397 " --> pdb=" O TRP D 393 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER D 399 " --> pdb=" O TYR D 395 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 439 removed outlier: 4.295A pdb=" N TYR D 429 " --> pdb=" O MET D 425 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE D 430 " --> pdb=" O MET D 426 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA D 432 " --> pdb=" O ALA D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 445 Processing helix chain 'D' and resid 446 through 448 No H-bonds generated for 'chain 'D' and resid 446 through 448' Processing helix chain 'D' and resid 459 through 484 removed outlier: 3.820A pdb=" N ASN D 465 " --> pdb=" O PRO D 461 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU D 466 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE D 467 " --> pdb=" O TYR D 463 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN D 468 " --> pdb=" O THR D 464 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA D 473 " --> pdb=" O LYS D 469 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 476 " --> pdb=" O VAL D 472 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE D 479 " --> pdb=" O VAL D 475 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE D 480 " --> pdb=" O VAL D 476 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA D 481 " --> pdb=" O CYS D 477 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 482 " --> pdb=" O THR D 478 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL D 484 " --> pdb=" O ILE D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 removed outlier: 3.937A pdb=" N LEU D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 487 through 492' 576 hydrogen bonds defined for protein. 1692 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: 4.00 Time building geometry restraints manager: 6.04 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: 4083 1.34 - 1.46: 3418 1.46 - 1.58: 6699 1.58 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 14344 Sorted by residual: bond pdb=" CB ASN D 468 " pdb=" CG ASN D 468 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.82e+00 bond pdb=" CB ASN B 468 " pdb=" CG ASN B 468 " ideal model delta sigma weight residual 1.516 1.456 0.060 2.50e-02 1.60e+03 5.73e+00 bond pdb=" CB ASN C 468 " pdb=" CG ASN C 468 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.65e+00 bond pdb=" CB ASN A 468 " pdb=" CG ASN A 468 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.56e+00 bond pdb=" C GLY D 118 " pdb=" N LEU D 119 " ideal model delta sigma weight residual 1.333 1.296 0.037 1.73e-02 3.34e+03 4.58e+00 ... (remaining 14339 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.56: 275 105.56 - 112.71: 7277 112.71 - 119.86: 5556 119.86 - 127.01: 6251 127.01 - 134.16: 193 Bond angle restraints: 19552 Sorted by residual: angle pdb=" N THR C 161 " pdb=" CA THR C 161 " pdb=" C THR C 161 " ideal model delta sigma weight residual 109.81 119.00 -9.19 2.21e+00 2.05e-01 1.73e+01 angle pdb=" N THR B 161 " pdb=" CA THR B 161 " pdb=" C THR B 161 " ideal model delta sigma weight residual 109.81 118.96 -9.15 2.21e+00 2.05e-01 1.72e+01 angle pdb=" N THR D 161 " pdb=" CA THR D 161 " pdb=" C THR D 161 " ideal model delta sigma weight residual 109.81 118.93 -9.12 2.21e+00 2.05e-01 1.70e+01 angle pdb=" N THR A 161 " pdb=" CA THR A 161 " pdb=" C THR A 161 " ideal model delta sigma weight residual 109.81 118.93 -9.12 2.21e+00 2.05e-01 1.70e+01 angle pdb=" C ASP B 46 " pdb=" N ASP B 47 " pdb=" CA ASP B 47 " ideal model delta sigma weight residual 121.54 129.09 -7.55 1.91e+00 2.74e-01 1.56e+01 ... (remaining 19547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.02: 7199 14.02 - 28.03: 785 28.03 - 42.05: 108 42.05 - 56.06: 12 56.06 - 70.07: 8 Dihedral angle restraints: 8112 sinusoidal: 2832 harmonic: 5280 Sorted by residual: dihedral pdb=" CA LYS A 359 " pdb=" C LYS A 359 " pdb=" N PHE A 360 " pdb=" CA PHE A 360 " ideal model delta harmonic sigma weight residual 180.00 143.52 36.48 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" CA LYS B 359 " pdb=" C LYS B 359 " pdb=" N PHE B 360 " pdb=" CA PHE B 360 " ideal model delta harmonic sigma weight residual 180.00 143.53 36.47 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" CA LYS D 359 " pdb=" C LYS D 359 " pdb=" N PHE D 360 " pdb=" CA PHE D 360 " ideal model delta harmonic sigma weight residual 180.00 143.56 36.44 0 5.00e+00 4.00e-02 5.31e+01 ... (remaining 8109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1589 0.060 - 0.120: 585 0.120 - 0.180: 94 0.180 - 0.240: 16 0.240 - 0.299: 4 Chirality restraints: 2288 Sorted by residual: chirality pdb=" CB VAL C 484 " pdb=" CA VAL C 484 " pdb=" CG1 VAL C 484 " pdb=" CG2 VAL C 484 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CB VAL A 484 " pdb=" CA VAL A 484 " pdb=" CG1 VAL A 484 " pdb=" CG2 VAL A 484 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB VAL B 484 " pdb=" CA VAL B 484 " pdb=" CG1 VAL B 484 " pdb=" CG2 VAL B 484 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 2285 not shown) Planarity restraints: 2388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 161 " 0.091 5.00e-02 4.00e+02 1.38e-01 3.04e+01 pdb=" N PRO B 162 " -0.238 5.00e-02 4.00e+02 pdb=" CA PRO B 162 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO B 162 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 161 " -0.091 5.00e-02 4.00e+02 1.38e-01 3.04e+01 pdb=" N PRO D 162 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO D 162 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO D 162 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 161 " -0.091 5.00e-02 4.00e+02 1.38e-01 3.03e+01 pdb=" N PRO C 162 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO C 162 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO C 162 " -0.074 5.00e-02 4.00e+02 ... (remaining 2385 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3615 2.78 - 3.31: 14332 3.31 - 3.84: 21481 3.84 - 4.37: 26880 4.37 - 4.90: 40916 Nonbonded interactions: 107224 Sorted by model distance: nonbonded pdb=" O ASN B 51 " pdb=" OG SER B 55 " model vdw 2.250 2.440 nonbonded pdb=" O ASN D 51 " pdb=" OG SER D 55 " model vdw 2.250 2.440 nonbonded pdb=" O ASN C 51 " pdb=" OG SER C 55 " model vdw 2.250 2.440 nonbonded pdb=" O ASN A 51 " pdb=" OG SER A 55 " model vdw 2.250 2.440 nonbonded pdb=" O SER B 433 " pdb=" OG SER B 436 " model vdw 2.254 2.440 ... (remaining 107219 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 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: 2.120 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: 6.940 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 35.820 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.084 14344 Z= 0.618 Angle : 1.257 9.674 19552 Z= 0.683 Chirality : 0.061 0.299 2288 Planarity : 0.011 0.138 2388 Dihedral : 11.774 70.075 4744 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 5.31 % Allowed : 11.17 % Favored : 83.52 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.45 % 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: -4.78 (0.16), residues: 1808 helix: -3.53 (0.10), residues: 960 sheet: None (None), residues: 0 loop : -2.61 (0.22), residues: 848 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 512 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 0 residues processed: 516 average time/residue: 0.2288 time to fit residues: 174.7829 Evaluate side-chains 330 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 1.424 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 107 optimal weight: 0.0770 chunk 167 optimal weight: 0.3980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 324 GLN A 329 ASN B 151 ASN B 324 GLN B 329 ASN C 151 ASN C 324 GLN D 151 ASN D 324 GLN D 329 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 14344 Z= 0.190 Angle : 0.721 8.920 19552 Z= 0.375 Chirality : 0.042 0.204 2288 Planarity : 0.007 0.099 2388 Dihedral : 7.426 43.303 1956 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 1.11 % Allowed : 8.74 % Favored : 90.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % Twisted General : 0.23 % 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 (0.17), residues: 1808 helix: -2.33 (0.12), residues: 1136 sheet: None (None), residues: 0 loop : -2.76 (0.24), residues: 672 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 478 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 478 average time/residue: 0.2358 time to fit residues: 170.1232 Evaluate side-chains 362 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 362 time to evaluate : 1.445 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 167 optimal weight: 0.0870 chunk 180 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 165 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 134 optimal weight: 0.0060 overall best weight: 0.7976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN C 117 ASN D 117 ASN ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 14344 Z= 0.179 Angle : 0.666 7.973 19552 Z= 0.341 Chirality : 0.041 0.211 2288 Planarity : 0.006 0.096 2388 Dihedral : 6.495 42.641 1956 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.96 % Favored : 90.15 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -2.60 (0.19), residues: 1808 helix: -1.41 (0.14), residues: 1112 sheet: None (None), residues: 0 loop : -2.06 (0.25), residues: 696 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 448 time to evaluate : 1.605 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 outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.2349 time to fit residues: 155.6582 Evaluate side-chains 354 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 1.457 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 0.0970 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 79 optimal weight: 0.0870 chunk 112 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 87 optimal weight: 0.3980 chunk 159 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.9158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 GLN A 468 ASN B 379 GLN ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 GLN C 468 ASN D 379 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 14344 Z= 0.172 Angle : 0.634 7.369 19552 Z= 0.326 Chirality : 0.041 0.220 2288 Planarity : 0.006 0.093 2388 Dihedral : 6.111 42.509 1956 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.52 % Favored : 91.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -1.98 (0.20), residues: 1808 helix: -1.07 (0.14), residues: 1144 sheet: None (None), residues: 0 loop : -1.52 (0.27), residues: 664 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.2340 time to fit residues: 157.4587 Evaluate side-chains 340 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 340 time to evaluate : 1.321 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 132 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN B 324 GLN C 324 GLN C 329 ASN D 324 GLN ** D 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 14344 Z= 0.164 Angle : 0.622 7.933 19552 Z= 0.314 Chirality : 0.040 0.222 2288 Planarity : 0.006 0.092 2388 Dihedral : 5.751 41.042 1956 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.86 % Favored : 92.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -1.59 (0.20), residues: 1808 helix: -0.65 (0.15), residues: 1136 sheet: None (None), residues: 0 loop : -1.60 (0.27), residues: 672 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 455 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.2261 time to fit residues: 155.2520 Evaluate side-chains 349 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 1.496 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 3.9990 chunk 160 optimal weight: 0.0000 chunk 35 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 14 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 195 ASN B 329 ASN C 195 ASN D 195 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 14344 Z= 0.153 Angle : 0.601 6.790 19552 Z= 0.305 Chirality : 0.041 0.240 2288 Planarity : 0.006 0.089 2388 Dihedral : 5.517 40.660 1956 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.08 % Favored : 93.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -1.36 (0.20), residues: 1808 helix: -0.38 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -1.71 (0.27), residues: 660 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.2237 time to fit residues: 157.0912 Evaluate side-chains 365 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 1.511 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 177 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN B 195 ASN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 GLN ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 379 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 14344 Z= 0.209 Angle : 0.659 8.202 19552 Z= 0.335 Chirality : 0.042 0.259 2288 Planarity : 0.006 0.092 2388 Dihedral : 5.795 40.507 1956 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.30 % Favored : 90.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -1.17 (0.20), residues: 1808 helix: -0.39 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -1.29 (0.27), residues: 660 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.2213 time to fit residues: 148.9866 Evaluate side-chains 359 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 1.525 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 87 optimal weight: 0.0970 chunk 16 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 169 ASN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN B 195 ASN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN C 169 ASN ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN D 195 ASN ** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 14344 Z= 0.168 Angle : 0.640 7.063 19552 Z= 0.325 Chirality : 0.041 0.257 2288 Planarity : 0.006 0.089 2388 Dihedral : 5.590 40.577 1956 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.80 % Favored : 92.37 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -1.28 (0.20), residues: 1808 helix: -0.40 (0.15), residues: 1228 sheet: None (None), residues: 0 loop : -1.63 (0.29), residues: 580 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 446 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 447 average time/residue: 0.2145 time to fit residues: 147.2076 Evaluate side-chains 358 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 1.415 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.0570 chunk 155 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 149 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 GLN B 468 ASN C 51 ASN ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 14344 Z= 0.316 Angle : 0.772 8.608 19552 Z= 0.396 Chirality : 0.046 0.275 2288 Planarity : 0.006 0.093 2388 Dihedral : 6.506 41.758 1956 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.45 % Favored : 88.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -1.40 (0.20), residues: 1808 helix: -0.49 (0.15), residues: 1144 sheet: None (None), residues: 0 loop : -1.56 (0.26), residues: 664 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.2291 time to fit residues: 145.1700 Evaluate side-chains 360 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 5.9990 chunk 106 optimal weight: 0.0570 chunk 82 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 183 optimal weight: 0.0570 chunk 168 optimal weight: 0.0770 chunk 145 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN C 305 ASN ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN D 292 GLN ** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 14344 Z= 0.163 Angle : 0.673 8.913 19552 Z= 0.335 Chirality : 0.042 0.258 2288 Planarity : 0.006 0.089 2388 Dihedral : 5.573 40.531 1956 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.69 % Favored : 92.64 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -1.17 (0.20), residues: 1808 helix: -0.28 (0.15), residues: 1216 sheet: None (None), residues: 0 loop : -1.62 (0.28), residues: 592 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3616 Ramachandran restraints generated. 1808 Oldfield, 0 Emsley, 1808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 454 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 456 average time/residue: 0.2273 time to fit residues: 155.5884 Evaluate side-chains 356 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 1.421 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN C 51 ASN C 305 ASN ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 ASN ** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.144454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.124143 restraints weight = 25686.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.127217 restraints weight = 15266.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.129339 restraints weight = 10265.178| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 14344 Z= 0.267 Angle : 0.738 10.621 19552 Z= 0.375 Chirality : 0.044 0.276 2288 Planarity : 0.006 0.091 2388 Dihedral : 6.093 41.474 1956 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.66 % Allowed : 9.46 % Favored : 89.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.69 % 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: -1.24 (0.20), residues: 1808 helix: -0.36 (0.15), residues: 1176 sheet: None (None), residues: 0 loop : -1.54 (0.27), residues: 632 =============================================================================== Job complete usr+sys time: 3221.62 seconds wall clock time: 58 minutes 56.05 seconds (3536.05 seconds total)