Starting phenix.real_space_refine on Fri Aug 9 22:26:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vog_21263/08_2024/6vog_21263.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vog_21263/08_2024/6vog_21263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vog_21263/08_2024/6vog_21263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vog_21263/08_2024/6vog_21263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vog_21263/08_2024/6vog_21263.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vog_21263/08_2024/6vog_21263.cif" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 98 5.16 5 C 17048 2.51 5 N 4689 2.21 5 O 5288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 37": "OD1" <-> "OD2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 263": "OD1" <-> "OD2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 14": "NH1" <-> "NH2" Residue "B GLU 55": "OE1" <-> "OE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 230": "OD1" <-> "OD2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B ASP 404": "OD1" <-> "OD2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B GLU 460": "OE1" <-> "OE2" Residue "C ASP 37": "OD1" <-> "OD2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 230": "OD1" <-> "OD2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C GLU 484": "OE1" <-> "OE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D GLU 311": "OE1" <-> "OE2" Residue "D ASP 366": "OD1" <-> "OD2" Residue "D GLU 416": "OE1" <-> "OE2" Residue "D PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 347": "OD1" <-> "OD2" Residue "E ASP 366": "OD1" <-> "OD2" Residue "E TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 403": "OD1" <-> "OD2" Residue "E PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 83": "OD1" <-> "OD2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 265": "OE1" <-> "OE2" Residue "F PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 336": "OD1" <-> "OD2" Residue "F ASP 369": "OD1" <-> "OD2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 130": "OD1" <-> "OD2" Residue "d GLU 160": "OE1" <-> "OE2" Residue "d TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 77": "OE1" <-> "OE2" Residue "g PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 126": "OD1" <-> "OD2" Residue "g GLU 142": "OE1" <-> "OE2" Residue "g ASP 224": "OD1" <-> "OD2" Residue "g PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 287": "OD1" <-> "OD2" Residue "g GLU 332": "OE1" <-> "OE2" Residue "e ASP 45": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 27137 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3796 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3832 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 483} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3829 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 481} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 3589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3589 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 451} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 3600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3600 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3610 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 24, 'TRANS': 451} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1360 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 173} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2444 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 308} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "e" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 926 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.37, per 1000 atoms: 0.53 Number of scatterers: 27137 At special positions: 0 Unit cell: (131.04, 151.84, 133.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 P 14 15.00 O 5288 8.00 N 4689 7.00 C 17048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.81 Conformation dependent library (CDL) restraints added in 5.0 seconds 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6546 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 26 sheets defined 47.6% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.12 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.418A pdb=" N MET A 82 " --> pdb=" O ASP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 105 removed outlier: 3.649A pdb=" N TYR A 104 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 105 " --> pdb=" O GLU A 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 101 through 105' Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 175 through 187 Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 217 through 221 removed outlier: 4.215A pdb=" N GLU A 220 " --> pdb=" O GLY A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 288 through 289 No H-bonds generated for 'chain 'A' and resid 288 through 289' Processing helix chain 'A' and resid 290 through 301 removed outlier: 3.606A pdb=" N LEU A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 373 through 395 removed outlier: 4.422A pdb=" N LEU A 385 " --> pdb=" O GLY A 381 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLU A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 removed outlier: 5.507A pdb=" N GLN A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU A 411 " --> pdb=" O THR A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 444 Processing helix chain 'A' and resid 445 through 449 removed outlier: 3.763A pdb=" N SER A 448 " --> pdb=" O TYR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 469 removed outlier: 3.868A pdb=" N ARG A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 479 removed outlier: 3.983A pdb=" N GLN A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 499 removed outlier: 3.529A pdb=" N GLN A 495 " --> pdb=" O LYS A 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.978A pdb=" N THR B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 105 removed outlier: 3.958A pdb=" N TYR B 104 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 175 through 187 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 232 through 253 Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 283 through 287 Processing helix chain 'B' and resid 288 through 289 No H-bonds generated for 'chain 'B' and resid 288 through 289' Processing helix chain 'B' and resid 290 through 300 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.295A pdb=" N ALA B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 371 " --> pdb=" O GLY B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 395 removed outlier: 4.639A pdb=" N LYS B 382 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 422 Processing helix chain 'B' and resid 430 through 443 Processing helix chain 'B' and resid 453 through 469 Processing helix chain 'B' and resid 469 through 480 removed outlier: 4.014A pdb=" N GLN B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 502 removed outlier: 3.788A pdb=" N GLN B 495 " --> pdb=" O LYS B 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 18 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.702A pdb=" N ASP C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 221 removed outlier: 3.633A pdb=" N TYR C 221 " --> pdb=" O ALA C 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 218 through 221' Processing helix chain 'C' and resid 232 through 252 Proline residue: C 240 - end of helix removed outlier: 3.668A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.649A pdb=" N ALA C 286 " --> pdb=" O GLY C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 289 No H-bonds generated for 'chain 'C' and resid 288 through 289' Processing helix chain 'C' and resid 290 through 301 removed outlier: 3.696A pdb=" N ARG C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 326 Processing helix chain 'C' and resid 330 through 338 removed outlier: 4.150A pdb=" N ILE C 336 " --> pdb=" O PRO C 332 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER C 337 " --> pdb=" O THR C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 368 through 372 Processing helix chain 'C' and resid 373 through 381 Processing helix chain 'C' and resid 382 through 397 Processing helix chain 'C' and resid 404 through 421 Processing helix chain 'C' and resid 430 through 443 Processing helix chain 'C' and resid 453 through 469 Processing helix chain 'C' and resid 470 through 480 Processing helix chain 'C' and resid 483 through 503 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.756A pdb=" N LEU D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 Processing helix chain 'D' and resid 177 through 193 Processing helix chain 'D' and resid 205 through 219 Processing helix chain 'D' and resid 242 through 263 removed outlier: 5.250A pdb=" N GLY D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU D 251 " --> pdb=" O MET D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 290 Processing helix chain 'D' and resid 301 through 311 removed outlier: 3.603A pdb=" N GLU D 305 " --> pdb=" O THR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 333 removed outlier: 3.766A pdb=" N ASP D 332 " --> pdb=" O VAL D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 381 through 402 Processing helix chain 'D' and resid 404 through 409 Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 470 through 474 Processing helix chain 'D' and resid 479 through 495 Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 177 through 190 Processing helix chain 'E' and resid 205 through 219 Processing helix chain 'E' and resid 242 through 263 removed outlier: 3.939A pdb=" N ARG E 248 " --> pdb=" O GLY E 244 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY E 250 " --> pdb=" O ARG E 246 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU E 251 " --> pdb=" O MET E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 289 removed outlier: 3.509A pdb=" N PHE E 278 " --> pdb=" O ASN E 274 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 288 " --> pdb=" O GLU E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 313 Processing helix chain 'E' and resid 330 through 333 removed outlier: 4.111A pdb=" N ASP E 333 " --> pdb=" O PRO E 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 330 through 333' Processing helix chain 'E' and resid 336 through 343 Processing helix chain 'E' and resid 353 through 359 Processing helix chain 'E' and resid 376 through 381 Processing helix chain 'E' and resid 383 through 409 removed outlier: 4.831A pdb=" N ASP E 403 " --> pdb=" O LYS E 399 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 432 removed outlier: 4.761A pdb=" N THR E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA E 422 " --> pdb=" O ARG E 418 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 450 through 464 removed outlier: 3.660A pdb=" N SER E 463 " --> pdb=" O GLN E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 474 Processing helix chain 'E' and resid 479 through 496 Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 153 through 160 Processing helix chain 'F' and resid 178 through 190 Processing helix chain 'F' and resid 205 through 219 Processing helix chain 'F' and resid 242 through 263 removed outlier: 4.504A pdb=" N GLY F 250 " --> pdb=" O ARG F 246 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LEU F 251 " --> pdb=" O MET F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 290 removed outlier: 3.830A pdb=" N PHE F 278 " --> pdb=" O ASN F 274 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 336 through 346 removed outlier: 3.867A pdb=" N THR F 342 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 360 removed outlier: 3.742A pdb=" N ALA F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 381 Processing helix chain 'F' and resid 381 through 406 removed outlier: 3.904A pdb=" N THR F 394 " --> pdb=" O ARG F 390 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 431 Processing helix chain 'F' and resid 450 through 464 removed outlier: 4.223A pdb=" N PHE F 458 " --> pdb=" O THR F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 475 removed outlier: 3.965A pdb=" N PHE F 474 " --> pdb=" O GLU F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 493 Processing helix chain 'd' and resid 73 through 90 Processing helix chain 'd' and resid 91 through 107 Processing helix chain 'd' and resid 108 through 117 Processing helix chain 'd' and resid 121 through 137 Processing helix chain 'd' and resid 139 through 152 Processing helix chain 'd' and resid 153 through 156 removed outlier: 3.528A pdb=" N ASN d 156 " --> pdb=" O GLU d 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 153 through 156' Processing helix chain 'd' and resid 157 through 173 removed outlier: 4.208A pdb=" N ASP d 167 " --> pdb=" O ASN d 163 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 203 Processing helix chain 'd' and resid 237 through 248 removed outlier: 4.279A pdb=" N LEU d 248 " --> pdb=" O ILE d 244 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 100 removed outlier: 3.505A pdb=" N ALA g 63 " --> pdb=" O LYS g 59 " (cutoff:3.500A) Proline residue: g 84 - end of helix Processing helix chain 'g' and resid 132 through 152 removed outlier: 4.681A pdb=" N LEU g 138 " --> pdb=" O ASN g 134 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU g 151 " --> pdb=" O GLU g 147 " (cutoff:3.500A) Processing helix chain 'g' and resid 161 through 170 Processing helix chain 'g' and resid 187 through 204 removed outlier: 4.342A pdb=" N ILE g 194 " --> pdb=" O GLU g 190 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP g 197 " --> pdb=" O ALA g 193 " (cutoff:3.500A) Processing helix chain 'g' and resid 291 through 362 Proline residue: g 297 - end of helix removed outlier: 4.191A pdb=" N ASP g 328 " --> pdb=" O SER g 324 " (cutoff:3.500A) Processing helix chain 'e' and resid 83 through 87 removed outlier: 3.994A pdb=" N ASP e 86 " --> pdb=" O ARG e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 104 removed outlier: 3.626A pdb=" N LEU e 96 " --> pdb=" O ALA e 92 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU e 100 " --> pdb=" O LEU e 96 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 131 removed outlier: 3.857A pdb=" N GLU e 114 " --> pdb=" O ARG e 110 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN e 130 " --> pdb=" O VAL e 126 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR e 131 " --> pdb=" O GLU e 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 67 removed outlier: 3.564A pdb=" N LEU A 33 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG A 41 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLY A 73 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 63 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 26 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL F 61 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL F 65 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL F 77 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ALA F 34 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE F 23 " --> pdb=" O ALA F 34 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 100 removed outlier: 3.536A pdb=" N GLU A 126 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 225 through 227 removed outlier: 3.571A pdb=" N LEU A 258 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 23 through 27 removed outlier: 7.332A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN E 66 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU E 68 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL B 35 " --> pdb=" O LEU E 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 30 through 36 current: chain 'E' and resid 92 through 97 Processing sheet with id=AA5, first strand: chain 'E' and resid 23 through 27 removed outlier: 7.332A pdb=" N ARG E 75 " --> pdb=" O GLN E 66 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN E 66 " --> pdb=" O ARG E 75 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 61 through 68 current: chain 'B' and resid 53 through 55 removed outlier: 5.722A pdb=" N ALA B 64 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL B 75 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ILE B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG B 41 " --> pdb=" O LEU B 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 30 through 36 current: chain 'E' and resid 92 through 97 Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 100 removed outlier: 4.165A pdb=" N GLU B 126 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 108 through 109 removed outlier: 7.410A pdb=" N VAL B 225 " --> pdb=" O CYS B 194 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TYR B 196 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLU B 227 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA B 198 " --> pdb=" O GLU B 227 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE B 193 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ILE B 260 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 195 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR B 257 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 319 through 321 removed outlier: 3.546A pdb=" N VAL B 320 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 169 " --> pdb=" O LEU B 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'd' and resid 231 through 232 removed outlier: 3.860A pdb=" N VAL C 27 " --> pdb=" O LEU d 232 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ASN C 28 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE C 63 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY C 73 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU C 67 " --> pdb=" O ASN C 71 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N HIS C 43 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL C 32 " --> pdb=" O HIS C 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.685A pdb=" N VAL C 100 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU C 126 " --> pdb=" O VAL C 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 146 through 147 removed outlier: 4.529A pdb=" N VAL C 160 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 193 through 198 removed outlier: 5.882A pdb=" N ILE C 193 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE C 260 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL C 195 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP C 262 " --> pdb=" O VAL C 195 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 197 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR C 257 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N LEU C 317 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE C 259 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ILE C 319 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR C 261 " --> pdb=" O ILE C 319 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N GLU C 321 " --> pdb=" O TYR C 261 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE C 168 " --> pdb=" O PRO C 318 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY C 170 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU C 167 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU C 345 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE C 169 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 21 through 27 removed outlier: 4.942A pdb=" N ILE D 23 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE D 27 " --> pdb=" O VAL D 30 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 30 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL D 77 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL D 65 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN D 45 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ALA D 46 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS D 50 " --> pdb=" O GLU D 90 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLU D 90 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY D 21 " --> pdb=" O VAL D 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 99 through 101 Processing sheet with id=AB6, first strand: chain 'D' and resid 148 through 149 removed outlier: 3.883A pdb=" N TYR D 162 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 267 through 271 removed outlier: 5.671A pdb=" N VAL D 268 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE D 324 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU D 270 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE D 168 " --> pdb=" O GLN D 325 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR D 350 " --> pdb=" O LYS D 167 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY D 169 " --> pdb=" O THR D 350 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 200 through 204 removed outlier: 6.159A pdb=" N GLY D 201 " --> pdb=" O GLY D 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 99 through 101 Processing sheet with id=AC1, first strand: chain 'E' and resid 234 through 238 removed outlier: 3.947A pdb=" N GLY E 200 " --> pdb=" O PHE E 271 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU E 270 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ALA E 326 " --> pdb=" O LEU E 270 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE E 272 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N TYR E 328 " --> pdb=" O ILE E 272 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE E 168 " --> pdb=" O GLN E 325 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL E 327 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU E 170 " --> pdb=" O VAL E 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 99 through 101 Processing sheet with id=AC3, first strand: chain 'F' and resid 235 through 238 removed outlier: 7.465A pdb=" N VAL F 235 " --> pdb=" O SER F 197 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE F 199 " --> pdb=" O VAL F 235 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLY F 237 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLY F 201 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP F 273 " --> pdb=" O GLY F 200 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LYS F 167 " --> pdb=" O ALA F 348 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N THR F 350 " --> pdb=" O LYS F 167 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLY F 169 " --> pdb=" O THR F 350 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'd' and resid 178 through 179 removed outlier: 6.166A pdb=" N ALA d 178 " --> pdb=" O LYS d 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'g' and resid 178 through 180 removed outlier: 3.771A pdb=" N ARG g 178 " --> pdb=" O ILE g 157 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU g 120 " --> pdb=" O ILE g 158 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE g 160 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL g 122 " --> pdb=" O ILE g 160 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA g 119 " --> pdb=" O GLU g 211 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU g 213 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N MET g 121 " --> pdb=" O LEU g 213 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR g 214 " --> pdb=" O VAL g 226 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL g 226 " --> pdb=" O TYR g 214 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'g' and resid 253 through 258 removed outlier: 3.747A pdb=" N LEU g 254 " --> pdb=" O ASP g 269 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP g 269 " --> pdb=" O LEU g 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 283 through 284 removed outlier: 6.604A pdb=" N GLU g 283 " --> pdb=" O ALA e 41 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ALA e 43 " --> pdb=" O GLU g 283 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR e 42 " --> pdb=" O ALA e 67 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU e 3 " --> pdb=" O VAL e 19 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 24 through 26 1290 hydrogen bonds defined for protein. 3714 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: 9.41 Time building geometry restraints manager: 12.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8222 1.33 - 1.45: 3776 1.45 - 1.57: 15307 1.57 - 1.69: 23 1.69 - 1.81: 185 Bond restraints: 27513 Sorted by residual: bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.61e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.52e+01 bond pdb=" C4 ATP F 601 " pdb=" C5 ATP F 601 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.34e+01 bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.75e+01 bond pdb=" C5 ATP A 601 " pdb=" C6 ATP A 601 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.68e+01 ... (remaining 27508 not shown) Histogram of bond angle deviations from ideal: 98.45 - 106.17: 718 106.17 - 113.90: 16070 113.90 - 121.63: 14372 121.63 - 129.35: 6107 129.35 - 137.08: 60 Bond angle restraints: 37327 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 118.43 21.44 1.00e+00 1.00e+00 4.60e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 119.32 20.55 1.00e+00 1.00e+00 4.22e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.78 20.09 1.00e+00 1.00e+00 4.04e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 117.14 19.69 1.00e+00 1.00e+00 3.88e+02 angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 120.88 18.99 1.00e+00 1.00e+00 3.61e+02 ... (remaining 37322 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.61: 15609 23.61 - 47.22: 1133 47.22 - 70.84: 125 70.84 - 94.45: 48 94.45 - 118.06: 3 Dihedral angle restraints: 16918 sinusoidal: 6718 harmonic: 10200 Sorted by residual: dihedral pdb=" CA TYR D 362 " pdb=" C TYR D 362 " pdb=" N PRO D 363 " pdb=" CA PRO D 363 " ideal model delta harmonic sigma weight residual 180.00 120.03 59.97 0 5.00e+00 4.00e-02 1.44e+02 dihedral pdb=" CA ALA F 295 " pdb=" C ALA F 295 " pdb=" N VAL F 296 " pdb=" CA VAL F 296 " ideal model delta harmonic sigma weight residual -180.00 -126.80 -53.20 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA ALA D 295 " pdb=" C ALA D 295 " pdb=" N VAL D 296 " pdb=" CA VAL D 296 " ideal model delta harmonic sigma weight residual -180.00 -127.78 -52.22 0 5.00e+00 4.00e-02 1.09e+02 ... (remaining 16915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3958 0.090 - 0.181: 438 0.181 - 0.271: 24 0.271 - 0.361: 4 0.361 - 0.452: 1 Chirality restraints: 4425 Sorted by residual: chirality pdb=" CB ILE B 331 " pdb=" CA ILE B 331 " pdb=" CG1 ILE B 331 " pdb=" CG2 ILE B 331 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" CB ILE B 169 " pdb=" CA ILE B 169 " pdb=" CG1 ILE B 169 " pdb=" CG2 ILE B 169 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB ILE g 239 " pdb=" CA ILE g 239 " pdb=" CG1 ILE g 239 " pdb=" CG2 ILE g 239 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 3.06e+00 ... (remaining 4422 not shown) Planarity restraints: 4851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 362 " -0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO D 363 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 363 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 363 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 338 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO F 339 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO F 339 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 339 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 295 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C ALA D 295 " -0.045 2.00e-02 2.50e+03 pdb=" O ALA D 295 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL D 296 " 0.015 2.00e-02 2.50e+03 ... (remaining 4848 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6283 2.77 - 3.31: 29182 3.31 - 3.84: 50500 3.84 - 4.37: 57908 4.37 - 4.90: 93750 Nonbonded interactions: 237623 Sorted by model distance: nonbonded pdb=" OH TYR B 330 " pdb=" OE2 GLU D 284 " model vdw 2.242 3.040 nonbonded pdb=" O VAL D 102 " pdb=" OG1 THR D 128 " model vdw 2.243 3.040 nonbonded pdb=" O GLY F 450 " pdb=" OG1 THR F 454 " model vdw 2.252 3.040 nonbonded pdb=" OG1 THR A 228 " pdb=" OD1 ASP A 230 " model vdw 2.253 3.040 nonbonded pdb=" O ILE A 475 " pdb=" OG1 THR A 479 " model vdw 2.258 3.040 ... (remaining 237618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 15 or (resid 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 23 or (resid 24 through 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 322 or (resid 323 thro \ ugh 324 and (name N or name CA or name C or name O or name CB )) or resid 325 th \ rough 398 or (resid 399 through 400 and (name N or name CA or name C or name O o \ r name CB )) or resid 401 through 471 or (resid 472 and (name N or name CA or na \ me C or name O or name CB )) or resid 473 through 503 or resid 601)) selection = (chain 'B' and (resid 8 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 393 or (resid 394 thro \ ugh 397 and (name N or name CA or name C or name O or name CB )) or resid 398 or \ (resid 399 through 400 and (name N or name CA or name C or name O or name CB )) \ or resid 401 through 432 or (resid 433 and (name N or name CA or name C or name \ O or name CB )) or resid 434 through 503 or resid 601)) selection = (chain 'C' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 23 or (resid 24 through 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 322 or (resid 323 through 324 and ( \ name N or name CA or name C or name O or name CB )) or resid 325 through 393 or \ (resid 394 through 397 and (name N or name CA or name C or name O or name CB )) \ or resid 398 through 432 or (resid 433 and (name N or name CA or name C or name \ O or name CB )) or resid 434 through 471 or (resid 472 and (name N or name CA or \ name C or name O or name CB )) or resid 473 through 503 or resid 601)) } ncs_group { reference = (chain 'D' and (resid 19 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 58 or (resid 59 and ( \ name N or name CA or name C or name O or name CB )) or resid 60 through 115 or ( \ resid 116 and (name N or name CA or name C or name O or name CB )) or resid 117 \ through 118 or (resid 119 and (name N or name CA or name C or name O or name CB \ )) or resid 120 through 260 or (resid 261 and (name N or name CA or name C or na \ me O or name CB )) or resid 262 through 310 or (resid 311 and (name N or name CA \ or name C or name O or name CB )) or resid 312 through 407 or (resid 408 and (n \ ame N or name CA or name C or name O or name CB )) or resid 409 through 416 or ( \ resid 417 and (name N or name CA or name C or name O or name CB )) or resid 418 \ through 494)) selection = (chain 'E' and (resid 19 through 56 or (resid 57 and (name N or name CA or name \ C or name O or name CB )) or resid 58 through 78 or (resid 79 and (name N or nam \ e CA or name C or name O or name CB )) or resid 80 through 260 or (resid 261 and \ (name N or name CA or name C or name O or name CB )) or resid 262 through 331 o \ r (resid 332 through 333 and (name N or name CA or name C or name O or name CB ) \ ) or resid 334 through 407 or (resid 408 and (name N or name CA or name C or nam \ e O or name CB )) or resid 409 through 414 or (resid 415 and (name N or name CA \ or name C or name O or name CB )) or resid 416 through 446 or (resid 447 and (na \ me N or name CA or name C or name O or name CB )) or resid 448 through 464 or (r \ esid 465 and (name N or name CA or name C or name O or name CB )) or resid 466 t \ hrough 494)) selection = (chain 'F' and (resid 19 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 56 or (resid 57 and ( \ name N or name CA or name C or name O or name CB )) or resid 58 or (resid 59 and \ (name N or name CA or name C or name O or name CB )) or resid 60 through 78 or \ (resid 79 and (name N or name CA or name C or name O or name CB )) or resid 80 t \ hrough 115 or (resid 116 and (name N or name CA or name C or name O or name CB ) \ ) or resid 117 through 118 or (resid 119 and (name N or name CA or name C or nam \ e O or name CB )) or resid 120 through 310 or (resid 311 and (name N or name CA \ or name C or name O or name CB )) or resid 312 through 317 or (resid 318 and (na \ me N or name CA or name C or name O or name CB )) or resid 319 through 331 or (r \ esid 332 through 333 and (name N or name CA or name C or name O or name CB )) or \ resid 334 through 414 or (resid 415 and (name N or name CA or name C or name O \ or name CB )) or resid 416 or (resid 417 and (name N or name CA or name C or nam \ e O or name CB )) or resid 418 through 446 or (resid 447 and (name N or name CA \ or name C or name O or name CB )) or resid 448 through 464 or (resid 465 and (na \ me N or name CA or name C or name O or name CB )) or resid 466 through 494)) } 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: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 72.680 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 : 0.007 0.081 27513 Z= 0.437 Angle : 1.078 21.440 37327 Z= 0.658 Chirality : 0.056 0.452 4425 Planarity : 0.007 0.072 4851 Dihedral : 16.400 118.062 10369 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.80 % Favored : 91.11 % Rotamer: Outliers : 0.49 % Allowed : 13.12 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % Twisted General : 0.15 % 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: -3.94 (0.12), residues: 3544 helix: -2.16 (0.10), residues: 1482 sheet: -3.57 (0.20), residues: 441 loop : -2.68 (0.13), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP e 15 HIS 0.009 0.002 HIS C 256 PHE 0.037 0.003 PHE F 343 TYR 0.024 0.003 TYR A 271 ARG 0.017 0.001 ARG B 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 950 time to evaluate : 3.327 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7037 (tp30) cc_final: 0.6736 (tp30) REVERT: A 76 LEU cc_start: 0.9453 (mt) cc_final: 0.9224 (mt) REVERT: A 169 ILE cc_start: 0.8396 (tp) cc_final: 0.8183 (tp) REVERT: A 219 MET cc_start: 0.8268 (ppp) cc_final: 0.8001 (ppp) REVERT: A 230 ASP cc_start: 0.7896 (p0) cc_final: 0.7527 (p0) REVERT: A 251 MET cc_start: 0.8095 (tmm) cc_final: 0.7552 (ttp) REVERT: A 266 LYS cc_start: 0.8029 (mmtt) cc_final: 0.7569 (mmmm) REVERT: A 278 LEU cc_start: 0.7753 (mt) cc_final: 0.7481 (mt) REVERT: A 287 TYR cc_start: 0.7333 (m-80) cc_final: 0.7004 (m-80) REVERT: A 292 PHE cc_start: 0.8164 (t80) cc_final: 0.7617 (t80) REVERT: A 300 GLU cc_start: 0.8491 (tt0) cc_final: 0.8009 (mt-10) REVERT: A 309 LEU cc_start: 0.9223 (mm) cc_final: 0.8992 (tt) REVERT: A 314 MET cc_start: 0.7629 (ttm) cc_final: 0.7293 (ttp) REVERT: A 333 THR cc_start: 0.9105 (t) cc_final: 0.8714 (t) REVERT: A 349 LEU cc_start: 0.9243 (mt) cc_final: 0.9024 (mt) REVERT: A 376 MET cc_start: 0.7723 (tpp) cc_final: 0.7417 (tpp) REVERT: A 436 MET cc_start: 0.9145 (ppp) cc_final: 0.8670 (ppp) REVERT: A 464 TYR cc_start: 0.7360 (t80) cc_final: 0.7144 (t80) REVERT: B 15 GLU cc_start: 0.9137 (tt0) cc_final: 0.8546 (mm-30) REVERT: B 147 LEU cc_start: 0.8826 (tt) cc_final: 0.8554 (tt) REVERT: B 194 CYS cc_start: 0.8989 (m) cc_final: 0.8561 (m) REVERT: B 278 LEU cc_start: 0.9333 (mm) cc_final: 0.9105 (mm) REVERT: B 293 TYR cc_start: 0.7062 (t80) cc_final: 0.6038 (t80) REVERT: B 360 VAL cc_start: 0.8372 (m) cc_final: 0.8156 (t) REVERT: B 386 GLU cc_start: 0.7975 (tp30) cc_final: 0.7273 (tm-30) REVERT: B 449 LEU cc_start: 0.7171 (mm) cc_final: 0.6669 (mm) REVERT: B 453 GLN cc_start: 0.9216 (mm110) cc_final: 0.8987 (mp10) REVERT: B 480 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8411 (mmtt) REVERT: C 14 ARG cc_start: 0.5918 (mmt90) cc_final: 0.5505 (mpt180) REVERT: C 49 MET cc_start: 0.7734 (tpt) cc_final: 0.6206 (tpt) REVERT: C 55 GLU cc_start: 0.8338 (tp30) cc_final: 0.8112 (tp30) REVERT: C 77 MET cc_start: 0.7670 (ppp) cc_final: 0.7435 (ppp) REVERT: C 108 VAL cc_start: 0.9053 (t) cc_final: 0.8658 (t) REVERT: C 194 CYS cc_start: 0.8645 (m) cc_final: 0.7560 (m) REVERT: C 219 MET cc_start: 0.8011 (ptm) cc_final: 0.7475 (ptm) REVERT: C 228 THR cc_start: 0.8442 (p) cc_final: 0.7960 (t) REVERT: C 251 MET cc_start: 0.8047 (ttp) cc_final: 0.6997 (ttp) REVERT: C 258 LEU cc_start: 0.9236 (tt) cc_final: 0.8991 (tt) REVERT: C 271 TYR cc_start: 0.8234 (t80) cc_final: 0.7957 (t80) REVERT: C 273 GLN cc_start: 0.8343 (tt0) cc_final: 0.7775 (tt0) REVERT: C 345 LEU cc_start: 0.7801 (mm) cc_final: 0.7004 (mp) REVERT: C 392 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8715 (tm-30) REVERT: C 433 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6703 (tp30) REVERT: C 434 GLN cc_start: 0.9076 (mt0) cc_final: 0.8529 (mt0) REVERT: C 436 MET cc_start: 0.8116 (mtt) cc_final: 0.7806 (mtt) REVERT: C 449 LEU cc_start: 0.8582 (mt) cc_final: 0.8150 (mt) REVERT: C 462 ARG cc_start: 0.8843 (ptm-80) cc_final: 0.8355 (ptm-80) REVERT: C 489 LEU cc_start: 0.9122 (mt) cc_final: 0.8365 (mt) REVERT: D 64 GLU cc_start: 0.7760 (mp0) cc_final: 0.7415 (mp0) REVERT: D 65 VAL cc_start: 0.7968 (t) cc_final: 0.7763 (t) REVERT: D 89 MET cc_start: 0.8012 (ttm) cc_final: 0.7669 (mtt) REVERT: D 182 ILE cc_start: 0.8629 (mt) cc_final: 0.8370 (mm) REVERT: D 199 PHE cc_start: 0.8957 (t80) cc_final: 0.8500 (t80) REVERT: D 204 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7554 (tm-30) REVERT: D 212 LEU cc_start: 0.9334 (tp) cc_final: 0.9077 (tt) REVERT: D 247 MET cc_start: 0.8862 (ttp) cc_final: 0.8326 (ttt) REVERT: D 335 THR cc_start: 0.8966 (t) cc_final: 0.8598 (m) REVERT: D 345 HIS cc_start: 0.7095 (t70) cc_final: 0.6093 (t70) REVERT: D 366 ASP cc_start: 0.8285 (t70) cc_final: 0.7973 (t0) REVERT: D 401 LEU cc_start: 0.8591 (mm) cc_final: 0.8343 (tt) REVERT: D 418 ARG cc_start: 0.8983 (ttp80) cc_final: 0.8570 (ttp80) REVERT: D 469 LEU cc_start: 0.8677 (mt) cc_final: 0.8470 (mt) REVERT: E 79 MET cc_start: 0.8198 (mpp) cc_final: 0.6688 (mpp) REVERT: E 102 VAL cc_start: 0.8652 (m) cc_final: 0.7999 (p) REVERT: E 251 LEU cc_start: 0.8052 (tp) cc_final: 0.7485 (tp) REVERT: E 264 ASN cc_start: 0.8133 (m110) cc_final: 0.7847 (t0) REVERT: E 328 TYR cc_start: 0.8422 (t80) cc_final: 0.8133 (t80) REVERT: E 386 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7954 (mm-30) REVERT: E 393 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7599 (tp30) REVERT: E 439 GLU cc_start: 0.8042 (pp20) cc_final: 0.7224 (pm20) REVERT: E 455 ILE cc_start: 0.9167 (pt) cc_final: 0.8801 (mm) REVERT: E 456 ARG cc_start: 0.8428 (tmt-80) cc_final: 0.8081 (tmm160) REVERT: F 168 ILE cc_start: 0.7662 (mm) cc_final: 0.7332 (mt) REVERT: F 213 TYR cc_start: 0.8482 (t80) cc_final: 0.8222 (t80) REVERT: F 214 MET cc_start: 0.8213 (mmp) cc_final: 0.7886 (tmm) REVERT: F 239 MET cc_start: 0.7905 (ttm) cc_final: 0.7424 (ttm) REVERT: F 306 MET cc_start: 0.8408 (tpp) cc_final: 0.7880 (tpt) REVERT: F 475 TYR cc_start: 0.7626 (t80) cc_final: 0.7392 (t80) REVERT: F 481 ASP cc_start: 0.8361 (m-30) cc_final: 0.8126 (m-30) REVERT: F 482 GLU cc_start: 0.8653 (tp30) cc_final: 0.8334 (tp30) REVERT: F 486 LYS cc_start: 0.8901 (tttp) cc_final: 0.8507 (tppp) REVERT: d 84 ASP cc_start: 0.8816 (t0) cc_final: 0.8551 (t0) REVERT: d 98 ASP cc_start: 0.8844 (t0) cc_final: 0.8543 (t0) REVERT: d 104 ARG cc_start: 0.8675 (tpt170) cc_final: 0.8327 (mmm-85) REVERT: d 112 TYR cc_start: 0.8711 (t80) cc_final: 0.8412 (t80) REVERT: d 114 PHE cc_start: 0.8966 (t80) cc_final: 0.8234 (t80) REVERT: d 125 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7709 (mtpp) REVERT: d 164 GLU cc_start: 0.7664 (mm-30) cc_final: 0.6178 (tp30) REVERT: d 167 ASP cc_start: 0.8860 (t70) cc_final: 0.8588 (p0) REVERT: d 193 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8514 (tt0) REVERT: d 235 MET cc_start: 0.7276 (ttp) cc_final: 0.7032 (ttp) REVERT: g 64 MET cc_start: 0.7920 (tpp) cc_final: 0.7420 (tpp) REVERT: g 96 MET cc_start: 0.8356 (mmp) cc_final: 0.7906 (mmm) REVERT: g 189 LYS cc_start: 0.8839 (mttp) cc_final: 0.8384 (mmmt) REVERT: g 287 ASP cc_start: 0.8787 (t70) cc_final: 0.8536 (m-30) REVERT: g 310 GLU cc_start: 0.8300 (tt0) cc_final: 0.7565 (tp30) REVERT: e 11 ASN cc_start: 0.8219 (p0) cc_final: 0.8014 (p0) REVERT: e 53 LEU cc_start: 0.6818 (tp) cc_final: 0.6614 (mt) REVERT: e 54 ASN cc_start: 0.8494 (m110) cc_final: 0.8211 (m-40) REVERT: e 124 THR cc_start: 0.8330 (m) cc_final: 0.7821 (m) REVERT: e 127 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7704 (mp0) outliers start: 14 outliers final: 5 residues processed: 958 average time/residue: 0.4112 time to fit residues: 611.4450 Evaluate side-chains 602 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 597 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 2.9990 chunk 266 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 319 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 66 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 342 GLN A 389 GLN A 497 GLN B 186 ASN B 256 HIS B 468 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 201 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN C 473 GLN ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN D 120 ASN D 433 GLN ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 GLN ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 ASN F 72 ASN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 489 ASN ** g 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 76 GLN g 286 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 309 GLN e 54 ASN e 56 GLN e 72 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 27513 Z= 0.256 Angle : 0.734 11.698 37327 Z= 0.380 Chirality : 0.047 0.240 4425 Planarity : 0.006 0.065 4851 Dihedral : 8.590 117.868 4002 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.39 % Favored : 92.58 % Rotamer: Outliers : 0.14 % Allowed : 5.93 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % Twisted General : 0.09 % 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: -2.79 (0.13), residues: 3544 helix: -0.89 (0.12), residues: 1485 sheet: -3.41 (0.19), residues: 480 loop : -2.19 (0.15), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 15 HIS 0.009 0.001 HIS D 345 PHE 0.033 0.002 PHE F 343 TYR 0.026 0.002 TYR A 221 ARG 0.019 0.001 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 782 time to evaluate : 3.396 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8334 (tt0) cc_final: 0.8016 (tt0) REVERT: A 57 GLU cc_start: 0.7225 (tp30) cc_final: 0.6886 (tp30) REVERT: A 61 ILE cc_start: 0.8756 (pt) cc_final: 0.8124 (pt) REVERT: A 77 MET cc_start: 0.8211 (mtp) cc_final: 0.7960 (mtp) REVERT: A 141 ARG cc_start: 0.8424 (tpp80) cc_final: 0.7823 (ttp80) REVERT: A 199 ILE cc_start: 0.8855 (mt) cc_final: 0.8615 (mt) REVERT: A 228 THR cc_start: 0.8280 (p) cc_final: 0.7909 (p) REVERT: A 251 MET cc_start: 0.8137 (tmm) cc_final: 0.7580 (tmm) REVERT: A 278 LEU cc_start: 0.8017 (mt) cc_final: 0.7769 (mt) REVERT: A 287 TYR cc_start: 0.7334 (m-80) cc_final: 0.7025 (m-10) REVERT: A 292 PHE cc_start: 0.8187 (t80) cc_final: 0.7770 (t80) REVERT: A 300 GLU cc_start: 0.8697 (tt0) cc_final: 0.8130 (mt-10) REVERT: A 304 LYS cc_start: 0.8810 (tttt) cc_final: 0.8192 (tptm) REVERT: A 436 MET cc_start: 0.9079 (ppp) cc_final: 0.8672 (ppp) REVERT: A 445 TYR cc_start: 0.5801 (t80) cc_final: 0.5568 (t80) REVERT: A 460 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8868 (mm-30) REVERT: A 498 MET cc_start: 0.8022 (mmm) cc_final: 0.7470 (tpt) REVERT: B 77 MET cc_start: 0.9001 (mtt) cc_final: 0.8701 (mtm) REVERT: B 157 MET cc_start: 0.8178 (mmm) cc_final: 0.7423 (tpp) REVERT: B 171 ASP cc_start: 0.7160 (t0) cc_final: 0.6833 (m-30) REVERT: B 194 CYS cc_start: 0.8924 (m) cc_final: 0.8628 (m) REVERT: B 274 MET cc_start: 0.8570 (ptm) cc_final: 0.8290 (tmm) REVERT: B 277 LEU cc_start: 0.8982 (mm) cc_final: 0.8754 (mm) REVERT: B 293 TYR cc_start: 0.7354 (t80) cc_final: 0.6304 (t80) REVERT: B 453 GLN cc_start: 0.9222 (mm110) cc_final: 0.8975 (mm-40) REVERT: B 480 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8395 (mmtt) REVERT: B 498 MET cc_start: 0.8379 (ttm) cc_final: 0.8127 (mtt) REVERT: C 14 ARG cc_start: 0.5943 (mmt90) cc_final: 0.5254 (mpt180) REVERT: C 15 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7562 (mm-30) REVERT: C 107 ARG cc_start: 0.7436 (mtt90) cc_final: 0.7225 (mtt90) REVERT: C 108 VAL cc_start: 0.9194 (t) cc_final: 0.8915 (t) REVERT: C 219 MET cc_start: 0.8414 (ptm) cc_final: 0.7735 (ptm) REVERT: C 251 MET cc_start: 0.7838 (ttp) cc_final: 0.6871 (ttp) REVERT: C 271 TYR cc_start: 0.8339 (t80) cc_final: 0.8023 (t80) REVERT: C 273 GLN cc_start: 0.8556 (tt0) cc_final: 0.7568 (tt0) REVERT: C 295 HIS cc_start: 0.8599 (m170) cc_final: 0.8357 (m170) REVERT: C 365 SER cc_start: 0.8954 (p) cc_final: 0.8695 (p) REVERT: C 385 LEU cc_start: 0.8069 (mt) cc_final: 0.7685 (mt) REVERT: C 433 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6596 (tp30) REVERT: C 434 GLN cc_start: 0.8914 (mt0) cc_final: 0.8693 (mt0) REVERT: C 436 MET cc_start: 0.8058 (mtt) cc_final: 0.7712 (mtt) REVERT: C 462 ARG cc_start: 0.8928 (ptm-80) cc_final: 0.8620 (ptm-80) REVERT: D 63 CYS cc_start: 0.8722 (m) cc_final: 0.8207 (m) REVERT: D 182 ILE cc_start: 0.8652 (mt) cc_final: 0.8450 (mm) REVERT: D 211 ASP cc_start: 0.7939 (m-30) cc_final: 0.7580 (m-30) REVERT: D 239 MET cc_start: 0.8446 (mmm) cc_final: 0.8103 (mmm) REVERT: D 247 MET cc_start: 0.8690 (ttp) cc_final: 0.8442 (ttt) REVERT: D 292 MET cc_start: 0.8225 (ttm) cc_final: 0.7854 (ttm) REVERT: D 311 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8394 (tm-30) REVERT: D 335 THR cc_start: 0.8974 (t) cc_final: 0.8669 (m) REVERT: D 345 HIS cc_start: 0.7361 (t70) cc_final: 0.7028 (t70) REVERT: D 366 ASP cc_start: 0.8467 (t70) cc_final: 0.7907 (t0) REVERT: D 453 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8211 (mm-30) REVERT: D 466 LEU cc_start: 0.8269 (tp) cc_final: 0.7750 (pt) REVERT: E 63 CYS cc_start: 0.8917 (p) cc_final: 0.8613 (p) REVERT: E 79 MET cc_start: 0.8328 (mpp) cc_final: 0.7408 (mpp) REVERT: E 120 ASN cc_start: 0.7934 (m-40) cc_final: 0.7579 (m-40) REVERT: E 128 THR cc_start: 0.8277 (p) cc_final: 0.7998 (p) REVERT: E 184 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8026 (pp20) REVERT: E 223 ASN cc_start: 0.8283 (t0) cc_final: 0.7900 (t0) REVERT: E 251 LEU cc_start: 0.8139 (tp) cc_final: 0.7677 (tp) REVERT: E 264 ASN cc_start: 0.8229 (m110) cc_final: 0.7569 (t0) REVERT: E 279 VAL cc_start: 0.9119 (t) cc_final: 0.8892 (t) REVERT: E 393 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8177 (tp30) REVERT: E 439 GLU cc_start: 0.8158 (pp20) cc_final: 0.7726 (pm20) REVERT: E 480 ILE cc_start: 0.8502 (tp) cc_final: 0.8240 (tp) REVERT: F 72 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8328 (p0) REVERT: F 145 LYS cc_start: 0.8307 (tptp) cc_final: 0.7588 (pttm) REVERT: F 168 ILE cc_start: 0.7556 (mm) cc_final: 0.7125 (mt) REVERT: F 184 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7969 (tp30) REVERT: F 206 THR cc_start: 0.7833 (t) cc_final: 0.7619 (t) REVERT: F 239 MET cc_start: 0.7849 (ttm) cc_final: 0.7477 (ttm) REVERT: F 247 MET cc_start: 0.8129 (tpt) cc_final: 0.7532 (tpt) REVERT: F 343 PHE cc_start: 0.7630 (p90) cc_final: 0.7382 (p90) REVERT: F 393 GLU cc_start: 0.7291 (mp0) cc_final: 0.6943 (mp0) REVERT: F 412 GLU cc_start: 0.5934 (mm-30) cc_final: 0.5344 (tp30) REVERT: F 481 ASP cc_start: 0.8351 (m-30) cc_final: 0.8085 (m-30) REVERT: F 482 GLU cc_start: 0.8563 (tp30) cc_final: 0.8167 (tp30) REVERT: F 486 LYS cc_start: 0.8911 (tttp) cc_final: 0.8560 (tppp) REVERT: d 98 ASP cc_start: 0.8881 (t0) cc_final: 0.8346 (t0) REVERT: d 104 ARG cc_start: 0.8594 (tpt170) cc_final: 0.8180 (mtm180) REVERT: d 112 TYR cc_start: 0.8387 (t80) cc_final: 0.8175 (t80) REVERT: d 114 PHE cc_start: 0.8983 (t80) cc_final: 0.8598 (t80) REVERT: d 125 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7861 (mttp) REVERT: d 139 GLN cc_start: 0.8694 (mm-40) cc_final: 0.7940 (mp10) REVERT: d 151 ASP cc_start: 0.8236 (m-30) cc_final: 0.7996 (m-30) REVERT: d 164 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7041 (tp30) REVERT: d 167 ASP cc_start: 0.8734 (t70) cc_final: 0.8484 (t70) REVERT: d 193 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8564 (tt0) REVERT: g 81 ASN cc_start: 0.8367 (t0) cc_final: 0.8056 (t0) REVERT: g 180 PHE cc_start: 0.7574 (t80) cc_final: 0.7265 (t80) REVERT: g 189 LYS cc_start: 0.8986 (mttp) cc_final: 0.8556 (mmmt) REVERT: g 260 LYS cc_start: 0.8335 (pttm) cc_final: 0.7930 (pttm) REVERT: g 320 MET cc_start: 0.6497 (ttm) cc_final: 0.6201 (tmm) REVERT: g 354 LEU cc_start: 0.8554 (tt) cc_final: 0.8245 (pp) REVERT: e 11 ASN cc_start: 0.8475 (p0) cc_final: 0.7671 (p0) REVERT: e 18 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8031 (mt-10) REVERT: e 19 VAL cc_start: 0.8405 (t) cc_final: 0.7901 (t) REVERT: e 114 GLU cc_start: 0.8277 (tt0) cc_final: 0.7836 (pt0) REVERT: e 124 THR cc_start: 0.8215 (m) cc_final: 0.7742 (m) REVERT: e 127 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7708 (mp0) outliers start: 4 outliers final: 1 residues processed: 786 average time/residue: 0.3935 time to fit residues: 481.0263 Evaluate side-chains 542 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 540 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 177 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 266 optimal weight: 0.9990 chunk 217 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 320 optimal weight: 4.9990 chunk 345 optimal weight: 20.0000 chunk 285 optimal weight: 3.9990 chunk 317 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 256 optimal weight: 6.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 342 GLN ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN B 497 GLN C 201 GLN ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN C 497 GLN ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN ** E 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN ** F 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN ** g 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 243 ASN g 309 GLN e 56 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 27513 Z= 0.357 Angle : 0.767 10.900 37327 Z= 0.395 Chirality : 0.048 0.250 4425 Planarity : 0.006 0.062 4851 Dihedral : 8.502 122.467 4002 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.10 % Allowed : 6.00 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % Twisted General : 0.09 % 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: -2.34 (0.14), residues: 3544 helix: -0.44 (0.13), residues: 1498 sheet: -3.32 (0.20), residues: 477 loop : -2.00 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP e 15 HIS 0.013 0.002 HIS D 345 PHE 0.027 0.002 PHE F 343 TYR 0.023 0.002 TYR E 298 ARG 0.018 0.001 ARG F 291 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 685 time to evaluate : 2.845 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8627 (tt0) cc_final: 0.7763 (tt0) REVERT: A 57 GLU cc_start: 0.7341 (tp30) cc_final: 0.7060 (tp30) REVERT: A 137 ILE cc_start: 0.7338 (mp) cc_final: 0.7062 (mp) REVERT: A 219 MET cc_start: 0.8401 (ppp) cc_final: 0.8163 (ppp) REVERT: A 251 MET cc_start: 0.8044 (tmm) cc_final: 0.7520 (tmm) REVERT: A 278 LEU cc_start: 0.8026 (mt) cc_final: 0.7765 (mt) REVERT: A 287 TYR cc_start: 0.7412 (m-80) cc_final: 0.7170 (m-10) REVERT: A 300 GLU cc_start: 0.8649 (tt0) cc_final: 0.7800 (mt-10) REVERT: A 314 MET cc_start: 0.8156 (ttp) cc_final: 0.7655 (ttp) REVERT: A 436 MET cc_start: 0.9174 (ppp) cc_final: 0.8709 (ppp) REVERT: A 445 TYR cc_start: 0.5788 (t80) cc_final: 0.5556 (t80) REVERT: A 498 MET cc_start: 0.8048 (mmm) cc_final: 0.7549 (tpt) REVERT: B 194 CYS cc_start: 0.9068 (m) cc_final: 0.8738 (m) REVERT: B 293 TYR cc_start: 0.7579 (t80) cc_final: 0.6648 (t80) REVERT: B 449 LEU cc_start: 0.7121 (mm) cc_final: 0.6439 (mm) REVERT: B 480 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8383 (mmtt) REVERT: C 14 ARG cc_start: 0.5795 (mmt90) cc_final: 0.5339 (mmt180) REVERT: C 45 LEU cc_start: 0.8741 (tp) cc_final: 0.8523 (tt) REVERT: C 49 MET cc_start: 0.8333 (tpt) cc_final: 0.7076 (tpt) REVERT: C 65 LEU cc_start: 0.9142 (mt) cc_final: 0.8873 (mp) REVERT: C 109 ILE cc_start: 0.9063 (mt) cc_final: 0.8863 (mm) REVERT: C 165 ARG cc_start: 0.5453 (ptp90) cc_final: 0.5183 (ptp-170) REVERT: C 219 MET cc_start: 0.8442 (ptm) cc_final: 0.7995 (ptm) REVERT: C 228 THR cc_start: 0.8186 (p) cc_final: 0.7897 (t) REVERT: C 251 MET cc_start: 0.7813 (ttp) cc_final: 0.6598 (ttp) REVERT: C 433 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6648 (tp30) REVERT: C 434 GLN cc_start: 0.8942 (mt0) cc_final: 0.8724 (mt0) REVERT: C 436 MET cc_start: 0.8094 (mtt) cc_final: 0.7887 (mtt) REVERT: D 63 CYS cc_start: 0.8791 (m) cc_final: 0.8195 (m) REVERT: D 64 GLU cc_start: 0.7391 (mp0) cc_final: 0.7098 (mp0) REVERT: D 89 MET cc_start: 0.8994 (mtp) cc_final: 0.8779 (mtp) REVERT: D 236 TYR cc_start: 0.4739 (t80) cc_final: 0.4453 (t80) REVERT: D 239 MET cc_start: 0.8452 (mmm) cc_final: 0.8000 (mmm) REVERT: D 247 MET cc_start: 0.8856 (ttp) cc_final: 0.8485 (ttm) REVERT: D 292 MET cc_start: 0.8299 (ttm) cc_final: 0.7814 (ttm) REVERT: D 311 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8175 (tm-30) REVERT: D 335 THR cc_start: 0.8910 (t) cc_final: 0.8653 (m) REVERT: D 345 HIS cc_start: 0.7542 (t70) cc_final: 0.6690 (t70) REVERT: D 366 ASP cc_start: 0.8562 (t70) cc_final: 0.8272 (t0) REVERT: D 453 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8261 (mm-30) REVERT: D 469 LEU cc_start: 0.8679 (mt) cc_final: 0.8376 (mt) REVERT: E 64 GLU cc_start: 0.7293 (pm20) cc_final: 0.6914 (pm20) REVERT: E 79 MET cc_start: 0.8428 (mpp) cc_final: 0.7788 (mpp) REVERT: E 120 ASN cc_start: 0.7839 (m-40) cc_final: 0.7497 (m-40) REVERT: E 128 THR cc_start: 0.8299 (p) cc_final: 0.8055 (p) REVERT: E 204 GLU cc_start: 0.7868 (tp30) cc_final: 0.6773 (tp30) REVERT: E 251 LEU cc_start: 0.8317 (tp) cc_final: 0.7833 (tp) REVERT: E 283 SER cc_start: 0.8290 (p) cc_final: 0.8055 (t) REVERT: E 299 GLN cc_start: 0.8732 (pm20) cc_final: 0.8080 (pm20) REVERT: E 327 VAL cc_start: 0.8925 (t) cc_final: 0.8571 (t) REVERT: E 393 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8080 (tp30) REVERT: E 396 GLN cc_start: 0.9121 (tp40) cc_final: 0.8725 (tp40) REVERT: E 439 GLU cc_start: 0.8166 (pp20) cc_final: 0.7738 (pm20) REVERT: F 145 LYS cc_start: 0.8569 (tptp) cc_final: 0.7981 (pttm) REVERT: F 239 MET cc_start: 0.7752 (ttm) cc_final: 0.7228 (ttm) REVERT: F 311 GLU cc_start: 0.8540 (tp30) cc_final: 0.8085 (tp30) REVERT: F 343 PHE cc_start: 0.8006 (p90) cc_final: 0.7771 (p90) REVERT: F 374 MET cc_start: 0.8753 (mmt) cc_final: 0.8485 (mpp) REVERT: F 402 GLN cc_start: 0.8683 (tp40) cc_final: 0.8475 (tp40) REVERT: F 412 GLU cc_start: 0.6314 (mm-30) cc_final: 0.5746 (tp30) REVERT: F 481 ASP cc_start: 0.8474 (m-30) cc_final: 0.8222 (m-30) REVERT: F 482 GLU cc_start: 0.8589 (tp30) cc_final: 0.8307 (tp30) REVERT: F 486 LYS cc_start: 0.8906 (tttp) cc_final: 0.8585 (tppp) REVERT: d 112 TYR cc_start: 0.8412 (t80) cc_final: 0.8182 (t80) REVERT: d 114 PHE cc_start: 0.9097 (t80) cc_final: 0.8817 (t80) REVERT: d 125 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7927 (mttp) REVERT: d 138 LEU cc_start: 0.7488 (mt) cc_final: 0.7181 (mp) REVERT: d 139 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8146 (mp10) REVERT: d 164 GLU cc_start: 0.7998 (mm-30) cc_final: 0.6772 (tp30) REVERT: d 193 GLN cc_start: 0.8976 (tp-100) cc_final: 0.8558 (tt0) REVERT: g 189 LYS cc_start: 0.9039 (mttp) cc_final: 0.8545 (mmmt) REVERT: g 320 MET cc_start: 0.6683 (ttm) cc_final: 0.6166 (tmm) REVERT: g 354 LEU cc_start: 0.8544 (tt) cc_final: 0.8236 (pp) REVERT: e 18 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8129 (mt-10) REVERT: e 19 VAL cc_start: 0.8456 (t) cc_final: 0.8070 (t) REVERT: e 114 GLU cc_start: 0.8287 (tt0) cc_final: 0.7972 (pt0) REVERT: e 124 THR cc_start: 0.8139 (m) cc_final: 0.7671 (m) REVERT: e 127 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7674 (mp0) outliers start: 3 outliers final: 0 residues processed: 687 average time/residue: 0.4142 time to fit residues: 456.5958 Evaluate side-chains 515 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 316 optimal weight: 0.7980 chunk 240 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 321 optimal weight: 7.9990 chunk 340 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 304 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN C 236 GLN ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 299 GLN F 396 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 309 GLN g 331 ASN e 56 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 27513 Z= 0.310 Angle : 0.747 10.958 37327 Z= 0.382 Chirality : 0.047 0.231 4425 Planarity : 0.005 0.064 4851 Dihedral : 8.411 124.314 4002 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 0.68 % Twisted General : 0.09 % 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: -2.11 (0.14), residues: 3544 helix: -0.17 (0.13), residues: 1487 sheet: -3.23 (0.20), residues: 502 loop : -1.91 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP e 15 HIS 0.008 0.001 HIS D 345 PHE 0.034 0.002 PHE A 292 TYR 0.021 0.002 TYR B 457 ARG 0.008 0.001 ARG F 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 679 time to evaluate : 3.076 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8605 (tt0) cc_final: 0.8096 (tt0) REVERT: A 53 LEU cc_start: 0.9253 (tt) cc_final: 0.9046 (tt) REVERT: A 57 GLU cc_start: 0.7460 (tp30) cc_final: 0.7198 (tp30) REVERT: A 77 MET cc_start: 0.7891 (mtp) cc_final: 0.7580 (mtp) REVERT: A 137 ILE cc_start: 0.7456 (mp) cc_final: 0.7119 (mp) REVERT: A 138 MET cc_start: 0.7840 (tpp) cc_final: 0.7502 (tpp) REVERT: A 219 MET cc_start: 0.8366 (ppp) cc_final: 0.8153 (ppp) REVERT: A 251 MET cc_start: 0.8046 (tmm) cc_final: 0.7493 (tmm) REVERT: A 285 GLU cc_start: 0.8235 (tt0) cc_final: 0.7818 (tt0) REVERT: A 300 GLU cc_start: 0.8725 (tt0) cc_final: 0.7677 (tt0) REVERT: A 314 MET cc_start: 0.8057 (ttp) cc_final: 0.7455 (ttp) REVERT: A 436 MET cc_start: 0.9095 (ppp) cc_final: 0.8661 (ppp) REVERT: A 445 TYR cc_start: 0.5767 (t80) cc_final: 0.5414 (t80) REVERT: A 498 MET cc_start: 0.8488 (tpt) cc_final: 0.8050 (tpt) REVERT: B 76 LEU cc_start: 0.9607 (mm) cc_final: 0.9365 (mm) REVERT: B 147 LEU cc_start: 0.8782 (tt) cc_final: 0.8483 (tt) REVERT: B 157 MET cc_start: 0.7849 (mmm) cc_final: 0.7638 (tpp) REVERT: B 274 MET cc_start: 0.8772 (ptm) cc_final: 0.8438 (tmm) REVERT: B 277 LEU cc_start: 0.8947 (mm) cc_final: 0.8737 (mm) REVERT: B 293 TYR cc_start: 0.7604 (t80) cc_final: 0.6703 (t80) REVERT: B 453 GLN cc_start: 0.9213 (mm110) cc_final: 0.8935 (tt0) REVERT: B 480 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8225 (mmtt) REVERT: B 482 PHE cc_start: 0.7650 (p90) cc_final: 0.7217 (p90) REVERT: C 55 GLU cc_start: 0.8212 (tp30) cc_final: 0.8007 (tp30) REVERT: C 107 ARG cc_start: 0.7797 (mtt90) cc_final: 0.7353 (mtm-85) REVERT: C 157 MET cc_start: 0.7993 (ptp) cc_final: 0.7786 (ptp) REVERT: C 219 MET cc_start: 0.8454 (ptm) cc_final: 0.8010 (ptm) REVERT: C 228 THR cc_start: 0.8572 (p) cc_final: 0.7847 (t) REVERT: C 259 ILE cc_start: 0.8931 (pt) cc_final: 0.8476 (pt) REVERT: C 262 ASP cc_start: 0.8410 (t0) cc_final: 0.7330 (p0) REVERT: C 274 MET cc_start: 0.8545 (mmm) cc_final: 0.8305 (mmm) REVERT: C 293 TYR cc_start: 0.8852 (t80) cc_final: 0.8651 (t80) REVERT: C 301 ARG cc_start: 0.7260 (ttm170) cc_final: 0.6970 (mtp85) REVERT: C 436 MET cc_start: 0.8052 (mtt) cc_final: 0.7810 (mtt) REVERT: C 485 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8098 (tm-30) REVERT: D 40 MET cc_start: 0.8252 (mmm) cc_final: 0.8039 (mmm) REVERT: D 63 CYS cc_start: 0.8883 (m) cc_final: 0.8211 (m) REVERT: D 64 GLU cc_start: 0.7474 (mp0) cc_final: 0.7223 (mp0) REVERT: D 89 MET cc_start: 0.8865 (mtp) cc_final: 0.8626 (mtp) REVERT: D 199 PHE cc_start: 0.8842 (t80) cc_final: 0.8456 (t80) REVERT: D 204 GLU cc_start: 0.8319 (tp30) cc_final: 0.7738 (tp30) REVERT: D 239 MET cc_start: 0.8427 (mmm) cc_final: 0.7971 (mmt) REVERT: D 247 MET cc_start: 0.8765 (ttp) cc_final: 0.8328 (ttp) REVERT: D 271 PHE cc_start: 0.8398 (m-80) cc_final: 0.7767 (m-80) REVERT: D 285 VAL cc_start: 0.9094 (t) cc_final: 0.8879 (t) REVERT: D 335 THR cc_start: 0.8978 (t) cc_final: 0.8677 (m) REVERT: D 345 HIS cc_start: 0.7573 (t70) cc_final: 0.7313 (t70) REVERT: D 366 ASP cc_start: 0.8591 (t70) cc_final: 0.7577 (t0) REVERT: D 426 LYS cc_start: 0.8443 (mttm) cc_final: 0.7563 (mttm) REVERT: D 453 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8290 (mm-30) REVERT: D 466 LEU cc_start: 0.8462 (tp) cc_final: 0.8249 (tp) REVERT: D 467 ASP cc_start: 0.8459 (p0) cc_final: 0.8215 (p0) REVERT: D 469 LEU cc_start: 0.8658 (mt) cc_final: 0.8092 (mt) REVERT: E 79 MET cc_start: 0.8496 (mpp) cc_final: 0.7839 (mpp) REVERT: E 120 ASN cc_start: 0.7746 (m-40) cc_final: 0.7369 (m-40) REVERT: E 128 THR cc_start: 0.8377 (p) cc_final: 0.8141 (p) REVERT: E 204 GLU cc_start: 0.7680 (tp30) cc_final: 0.6692 (tp30) REVERT: E 251 LEU cc_start: 0.8373 (tp) cc_final: 0.7938 (tp) REVERT: E 299 GLN cc_start: 0.8746 (pm20) cc_final: 0.8064 (pm20) REVERT: E 396 GLN cc_start: 0.9167 (tp40) cc_final: 0.8625 (tp40) REVERT: E 439 GLU cc_start: 0.8216 (pp20) cc_final: 0.7347 (pm20) REVERT: F 87 ARG cc_start: 0.7689 (ptt-90) cc_final: 0.7182 (ptp90) REVERT: F 145 LYS cc_start: 0.8562 (tptp) cc_final: 0.8077 (pttm) REVERT: F 184 GLU cc_start: 0.8528 (tp30) cc_final: 0.8279 (mm-30) REVERT: F 239 MET cc_start: 0.7812 (ttm) cc_final: 0.7202 (ttm) REVERT: F 247 MET cc_start: 0.8486 (tpt) cc_final: 0.8111 (tpt) REVERT: F 402 GLN cc_start: 0.8837 (tp40) cc_final: 0.8527 (tp40) REVERT: F 486 LYS cc_start: 0.8808 (tttp) cc_final: 0.8476 (tppp) REVERT: d 98 ASP cc_start: 0.8591 (t0) cc_final: 0.8117 (t0) REVERT: d 104 ARG cc_start: 0.8566 (tpt170) cc_final: 0.8099 (mtm180) REVERT: d 112 TYR cc_start: 0.8444 (t80) cc_final: 0.8200 (t80) REVERT: d 114 PHE cc_start: 0.9177 (t80) cc_final: 0.8903 (t80) REVERT: d 125 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7993 (mttp) REVERT: d 139 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8019 (mp10) REVERT: d 151 ASP cc_start: 0.7778 (m-30) cc_final: 0.7524 (m-30) REVERT: d 193 GLN cc_start: 0.9024 (tp-100) cc_final: 0.8617 (tt0) REVERT: g 81 ASN cc_start: 0.8334 (t0) cc_final: 0.8040 (t0) REVERT: g 180 PHE cc_start: 0.7905 (t80) cc_final: 0.7561 (t80) REVERT: g 189 LYS cc_start: 0.8967 (mttp) cc_final: 0.8465 (mmmt) REVERT: g 232 PRO cc_start: 0.6923 (Cg_endo) cc_final: 0.6684 (Cg_exo) REVERT: g 320 MET cc_start: 0.6762 (ttm) cc_final: 0.6192 (tmm) REVERT: g 354 LEU cc_start: 0.8585 (tt) cc_final: 0.8287 (pp) REVERT: e 11 ASN cc_start: 0.8682 (p0) cc_final: 0.7954 (p0) REVERT: e 18 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8103 (mt-10) REVERT: e 19 VAL cc_start: 0.8533 (t) cc_final: 0.8175 (t) REVERT: e 80 ASP cc_start: 0.7634 (t0) cc_final: 0.7076 (t0) REVERT: e 114 GLU cc_start: 0.8249 (tt0) cc_final: 0.7971 (pt0) REVERT: e 124 THR cc_start: 0.7819 (m) cc_final: 0.7282 (m) outliers start: 1 outliers final: 0 residues processed: 680 average time/residue: 0.3874 time to fit residues: 416.4212 Evaluate side-chains 507 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 507 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 283 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 253 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 290 optimal weight: 0.7980 chunk 235 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 305 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN C 201 GLN C 497 GLN D 188 ASN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 ASN ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 GLN ** F 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 ASN F 299 GLN F 472 GLN d 141 HIS g 58 GLN g 134 ASN g 290 GLN ** g 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27513 Z= 0.224 Angle : 0.715 11.768 37327 Z= 0.359 Chirality : 0.047 0.262 4425 Planarity : 0.005 0.069 4851 Dihedral : 8.096 124.968 4002 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.11 % Cis-general : 0.21 % Twisted Proline : 1.37 % Twisted General : 0.09 % 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: -1.87 (0.14), residues: 3544 helix: 0.04 (0.13), residues: 1490 sheet: -3.13 (0.20), residues: 503 loop : -1.78 (0.16), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP e 15 HIS 0.008 0.001 HIS D 345 PHE 0.031 0.002 PHE A 292 TYR 0.023 0.002 TYR E 298 ARG 0.008 0.001 ARG C 172 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 696 time to evaluate : 3.162 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.8474 (tt0) cc_final: 0.8155 (tt0) REVERT: A 53 LEU cc_start: 0.9175 (tt) cc_final: 0.8973 (tt) REVERT: A 77 MET cc_start: 0.7803 (mtp) cc_final: 0.7526 (mtp) REVERT: A 138 MET cc_start: 0.7807 (tpp) cc_final: 0.7520 (tpp) REVERT: A 219 MET cc_start: 0.8351 (ppp) cc_final: 0.8115 (ppp) REVERT: A 251 MET cc_start: 0.8090 (tmm) cc_final: 0.7626 (tmm) REVERT: A 285 GLU cc_start: 0.8119 (tt0) cc_final: 0.7856 (tt0) REVERT: A 287 TYR cc_start: 0.7340 (m-80) cc_final: 0.7044 (m-10) REVERT: A 300 GLU cc_start: 0.8435 (tt0) cc_final: 0.8085 (mt-10) REVERT: A 314 MET cc_start: 0.7805 (ttp) cc_final: 0.7532 (ttp) REVERT: A 337 SER cc_start: 0.8964 (p) cc_final: 0.8634 (p) REVERT: A 351 ASN cc_start: 0.7805 (m-40) cc_final: 0.7510 (m-40) REVERT: A 498 MET cc_start: 0.8381 (tpt) cc_final: 0.7820 (tpt) REVERT: B 37 ASP cc_start: 0.7489 (m-30) cc_final: 0.6728 (m-30) REVERT: B 77 MET cc_start: 0.8957 (mtt) cc_final: 0.8726 (mtm) REVERT: B 194 CYS cc_start: 0.9011 (m) cc_final: 0.8732 (m) REVERT: B 274 MET cc_start: 0.8728 (ptm) cc_final: 0.7980 (tmm) REVERT: B 277 LEU cc_start: 0.9015 (mm) cc_final: 0.8772 (mt) REVERT: B 293 TYR cc_start: 0.7490 (t80) cc_final: 0.6607 (t80) REVERT: B 480 LYS cc_start: 0.8667 (mtmt) cc_final: 0.8166 (mmtt) REVERT: C 15 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7420 (mm-30) REVERT: C 55 GLU cc_start: 0.8235 (tp30) cc_final: 0.8030 (tp30) REVERT: C 219 MET cc_start: 0.8378 (ptm) cc_final: 0.7916 (ptm) REVERT: C 251 MET cc_start: 0.7893 (ttp) cc_final: 0.6999 (ttp) REVERT: C 314 MET cc_start: 0.8800 (tpt) cc_final: 0.8265 (tpp) REVERT: C 385 LEU cc_start: 0.8178 (mt) cc_final: 0.7968 (mt) REVERT: C 449 LEU cc_start: 0.8450 (mm) cc_final: 0.8213 (tp) REVERT: D 63 CYS cc_start: 0.8788 (m) cc_final: 0.8024 (m) REVERT: D 64 GLU cc_start: 0.7632 (mp0) cc_final: 0.7367 (mp0) REVERT: D 89 MET cc_start: 0.8751 (mtp) cc_final: 0.8551 (mtp) REVERT: D 204 GLU cc_start: 0.7915 (tp30) cc_final: 0.7470 (tp30) REVERT: D 239 MET cc_start: 0.8370 (mmm) cc_final: 0.7976 (mmm) REVERT: D 247 MET cc_start: 0.8779 (ttp) cc_final: 0.8298 (ttp) REVERT: D 284 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8145 (mm-30) REVERT: D 285 VAL cc_start: 0.9144 (t) cc_final: 0.8910 (t) REVERT: D 305 GLU cc_start: 0.7903 (tt0) cc_final: 0.7657 (tt0) REVERT: D 335 THR cc_start: 0.8924 (t) cc_final: 0.8613 (m) REVERT: D 366 ASP cc_start: 0.8556 (t70) cc_final: 0.8154 (t0) REVERT: D 418 ARG cc_start: 0.8983 (ttp80) cc_final: 0.8665 (ttm110) REVERT: D 426 LYS cc_start: 0.8439 (mttm) cc_final: 0.7549 (mttm) REVERT: D 453 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8249 (mm-30) REVERT: D 467 ASP cc_start: 0.8403 (p0) cc_final: 0.8115 (p0) REVERT: D 469 LEU cc_start: 0.8688 (mt) cc_final: 0.8440 (mt) REVERT: E 64 GLU cc_start: 0.7349 (pm20) cc_final: 0.6909 (pm20) REVERT: E 120 ASN cc_start: 0.7768 (m-40) cc_final: 0.7441 (m-40) REVERT: E 128 THR cc_start: 0.8349 (p) cc_final: 0.8133 (p) REVERT: E 204 GLU cc_start: 0.7629 (tp30) cc_final: 0.6852 (tp30) REVERT: E 251 LEU cc_start: 0.8274 (tp) cc_final: 0.7833 (tp) REVERT: E 299 GLN cc_start: 0.8440 (pm20) cc_final: 0.7819 (pm20) REVERT: E 385 TYR cc_start: 0.9196 (t80) cc_final: 0.8966 (t80) REVERT: E 439 GLU cc_start: 0.8182 (pp20) cc_final: 0.7735 (pm20) REVERT: E 475 TYR cc_start: 0.8260 (t80) cc_final: 0.7978 (t80) REVERT: F 79 MET cc_start: 0.8550 (mmt) cc_final: 0.8128 (mmm) REVERT: F 87 ARG cc_start: 0.7667 (ptt-90) cc_final: 0.7214 (ptp90) REVERT: F 145 LYS cc_start: 0.8553 (tptp) cc_final: 0.8158 (pttm) REVERT: F 184 GLU cc_start: 0.8458 (tp30) cc_final: 0.8145 (mm-30) REVERT: F 213 TYR cc_start: 0.8754 (t80) cc_final: 0.8028 (t80) REVERT: F 239 MET cc_start: 0.7691 (ttm) cc_final: 0.6851 (ttm) REVERT: F 247 MET cc_start: 0.8480 (tpt) cc_final: 0.8233 (tpt) REVERT: F 256 MET cc_start: 0.8580 (mmm) cc_final: 0.8256 (mmt) REVERT: F 328 TYR cc_start: 0.8084 (t80) cc_final: 0.7414 (t80) REVERT: F 374 MET cc_start: 0.8554 (mmt) cc_final: 0.8315 (mpp) REVERT: F 486 LYS cc_start: 0.8885 (tttp) cc_final: 0.8544 (tppp) REVERT: d 104 ARG cc_start: 0.8638 (tpt170) cc_final: 0.8150 (mtm180) REVERT: d 125 LYS cc_start: 0.8285 (mtpt) cc_final: 0.8034 (mttp) REVERT: d 139 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8293 (mp10) REVERT: d 151 ASP cc_start: 0.7810 (m-30) cc_final: 0.7521 (m-30) REVERT: d 154 ARG cc_start: 0.8263 (mmp80) cc_final: 0.7966 (mmp80) REVERT: d 164 GLU cc_start: 0.7981 (mm-30) cc_final: 0.6843 (tp30) REVERT: d 193 GLN cc_start: 0.8988 (tp-100) cc_final: 0.8597 (tt0) REVERT: g 81 ASN cc_start: 0.8336 (t0) cc_final: 0.8080 (t0) REVERT: g 180 PHE cc_start: 0.7869 (t80) cc_final: 0.7581 (t80) REVERT: g 189 LYS cc_start: 0.8994 (mttp) cc_final: 0.8507 (mmmt) REVERT: g 232 PRO cc_start: 0.6759 (Cg_endo) cc_final: 0.6523 (Cg_exo) REVERT: g 303 GLN cc_start: 0.8585 (tp40) cc_final: 0.8199 (tp40) REVERT: g 320 MET cc_start: 0.6851 (ttm) cc_final: 0.6323 (tmm) REVERT: g 354 LEU cc_start: 0.8520 (tt) cc_final: 0.8164 (pp) REVERT: e 11 ASN cc_start: 0.8771 (p0) cc_final: 0.8122 (p0) REVERT: e 19 VAL cc_start: 0.8550 (t) cc_final: 0.8183 (t) outliers start: 3 outliers final: 0 residues processed: 697 average time/residue: 0.3775 time to fit residues: 414.6562 Evaluate side-chains 505 residues out of total 2933 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 3.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 114 optimal weight: 0.5980 chunk 306 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 340 optimal weight: 8.9990 chunk 282 optimal weight: 8.9990 chunk 157 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: