Starting phenix.real_space_refine on Sun Feb 18 23:02:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjt_25931/02_2024/7tjt_25931_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjt_25931/02_2024/7tjt_25931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjt_25931/02_2024/7tjt_25931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjt_25931/02_2024/7tjt_25931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjt_25931/02_2024/7tjt_25931_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjt_25931/02_2024/7tjt_25931_updated.pdb" } resolution = 3.2 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= 0.004 sd= 0.246 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 3 5.21 5 S 33 5.16 5 C 14610 2.51 5 N 4038 2.21 5 O 4435 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ASP 335": "OD1" <-> "OD2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "A TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "B ASP 124": "OD1" <-> "OD2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B GLU 357": "OE1" <-> "OE2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C GLU 330": "OE1" <-> "OE2" Residue "C ASP 349": "OD1" <-> "OD2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "D ASP 288": "OD1" <-> "OD2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 422": "OE1" <-> "OE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E GLU 68": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E ASP 288": "OD1" <-> "OD2" Residue "E ASP 352": "OD1" <-> "OD2" Residue "F GLU 29": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F GLU 193": "OE1" <-> "OE2" Residue "F ASP 250": "OD1" <-> "OD2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "F TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 319": "OD1" <-> "OD2" Residue "F ASP 349": "OD1" <-> "OD2" Residue "F GLU 395": "OE1" <-> "OE2" Residue "F GLU 405": "OE1" <-> "OE2" Residue "G GLU 5": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G ASP 112": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23129 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3607 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 459} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 3606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3606 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 458} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3642 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 462} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3433 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 65 Chain: "E" Number of atoms: 3483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3483 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3497 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1760 Classifications: {'peptide': 253} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain breaks: 2 Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.30, per 1000 atoms: 0.53 Number of scatterers: 23129 At special positions: 0 Unit cell: (128.135, 128.135, 147.748, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 P 10 15.00 Mg 3 11.99 O 4435 8.00 N 4038 7.00 C 14610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.68 Conformation dependent library (CDL) restraints added in 4.4 seconds 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5630 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 131 helices and 22 sheets defined 44.2% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.897A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 227 through 230 removed outlier: 3.678A pdb=" N TYR A 230 " --> pdb=" O ALA A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 261 Proline residue: A 249 - end of helix removed outlier: 3.623A pdb=" N TRP A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 300 through 310 removed outlier: 4.572A pdb=" N ARG A 310 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 383 through 411 removed outlier: 3.681A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLN A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A 409 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N SER A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ASP A 411 " --> pdb=" O GLN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 429 removed outlier: 3.551A pdb=" N ARG A 425 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 454 through 457 removed outlier: 3.914A pdb=" N GLY A 457 " --> pdb=" O HIS A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 454 through 457' Processing helix chain 'A' and resid 460 through 474 removed outlier: 5.855A pdb=" N GLY A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER A 468 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 471 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 Processing helix chain 'A' and resid 493 through 507 Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 177 through 192 removed outlier: 3.912A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TRP B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 Processing helix chain 'B' and resid 227 through 230 removed outlier: 3.648A pdb=" N TYR B 230 " --> pdb=" O ALA B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 227 through 230' Processing helix chain 'B' and resid 242 through 261 Proline residue: B 249 - end of helix removed outlier: 4.073A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 298 through 310 removed outlier: 4.306A pdb=" N PHE B 301 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG B 306 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU B 309 " --> pdb=" O ARG B 306 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 310 " --> pdb=" O LEU B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 377 through 380 Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 393 through 406 removed outlier: 3.773A pdb=" N ALA B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 430 removed outlier: 3.536A pdb=" N ARG B 425 " --> pdb=" O VAL B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 451 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 454 through 457 removed outlier: 3.783A pdb=" N GLY B 457 " --> pdb=" O HIS B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 454 through 457' Processing helix chain 'B' and resid 460 through 477 removed outlier: 4.347A pdb=" N GLY B 464 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU B 467 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU B 471 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 475 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN B 477 " --> pdb=" O LEU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 488 Processing helix chain 'B' and resid 493 through 508 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.991A pdb=" N GLN C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 224 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 261 Proline residue: C 249 - end of helix removed outlier: 3.689A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 300 through 310 removed outlier: 4.592A pdb=" N ARG C 310 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 377 through 380 Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 392 through 407 removed outlier: 4.533A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 430 removed outlier: 3.605A pdb=" N ARG C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 451 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 460 through 477 removed outlier: 3.816A pdb=" N ILE C 463 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY C 464 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 467 " --> pdb=" O GLY C 464 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 468 " --> pdb=" O GLU C 465 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU C 471 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS C 475 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN C 477 " --> pdb=" O LEU C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 488 Processing helix chain 'C' and resid 493 through 507 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 163 through 177 Processing helix chain 'D' and resid 191 through 204 Processing helix chain 'D' and resid 226 through 245 removed outlier: 5.016A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 271 Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 285 through 295 removed outlier: 4.390A pdb=" N ARG D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 320 through 328 removed outlier: 4.336A pdb=" N HIS D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 removed outlier: 3.798A pdb=" N LEU D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 363 No H-bonds generated for 'chain 'D' and resid 360 through 363' Processing helix chain 'D' and resid 365 through 391 removed outlier: 4.950A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 395 No H-bonds generated for 'chain 'D' and resid 393 through 395' Processing helix chain 'D' and resid 398 through 414 removed outlier: 3.768A pdb=" N ARG D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 425 removed outlier: 3.855A pdb=" N VAL D 423 " --> pdb=" O VAL D 420 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR D 425 " --> pdb=" O GLU D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 445 Processing helix chain 'D' and resid 454 through 456 No H-bonds generated for 'chain 'D' and resid 454 through 456' Processing helix chain 'D' and resid 463 through 474 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 139 through 144 Processing helix chain 'E' and resid 163 through 177 Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 226 through 247 removed outlier: 4.820A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 271 Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 285 through 295 removed outlier: 4.443A pdb=" N ARG E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 320 through 326 Processing helix chain 'E' and resid 337 through 342 removed outlier: 4.158A pdb=" N LEU E 342 " --> pdb=" O GLY E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 363 No H-bonds generated for 'chain 'E' and resid 360 through 363' Processing helix chain 'E' and resid 365 through 391 removed outlier: 4.668A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE E 387 " --> pdb=" O SER E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 395 No H-bonds generated for 'chain 'E' and resid 393 through 395' Processing helix chain 'E' and resid 398 through 413 Processing helix chain 'E' and resid 419 through 425 removed outlier: 3.903A pdb=" N VAL E 423 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR E 425 " --> pdb=" O GLU E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 445 Processing helix chain 'E' and resid 454 through 457 Processing helix chain 'E' and resid 463 through 473 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 124 through 126 No H-bonds generated for 'chain 'F' and resid 124 through 126' Processing helix chain 'F' and resid 139 through 144 Processing helix chain 'F' and resid 163 through 178 removed outlier: 4.715A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 204 Processing helix chain 'F' and resid 226 through 229 No H-bonds generated for 'chain 'F' and resid 226 through 229' Processing helix chain 'F' and resid 232 through 245 Processing helix chain 'F' and resid 258 through 269 removed outlier: 3.613A pdb=" N THR F 262 " --> pdb=" O ILE F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 280 No H-bonds generated for 'chain 'F' and resid 278 through 280' Processing helix chain 'F' and resid 283 through 295 removed outlier: 4.622A pdb=" N ALA F 286 " --> pdb=" O PRO F 283 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU F 294 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 320 through 328 removed outlier: 4.223A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 342 removed outlier: 3.837A pdb=" N LEU F 342 " --> pdb=" O GLY F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 383 removed outlier: 7.382A pdb=" N GLN F 365 " --> pdb=" O ALA F 361 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N GLU F 366 " --> pdb=" O VAL F 362 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N HIS F 367 " --> pdb=" O VAL F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 390 Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 398 through 414 Processing helix chain 'F' and resid 420 through 425 removed outlier: 3.650A pdb=" N VAL F 423 " --> pdb=" O VAL F 420 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR F 425 " --> pdb=" O GLU F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'F' and resid 454 through 457 Processing helix chain 'F' and resid 462 through 474 Processing helix chain 'G' and resid 3 through 54 removed outlier: 3.712A pdb=" N SER G 32 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA G 37 " --> pdb=" O LYS G 33 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 101 removed outlier: 4.114A pdb=" N ASP G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 120 Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 185 through 188 No H-bonds generated for 'chain 'G' and resid 185 through 188' Processing helix chain 'G' and resid 205 through 274 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.783A pdb=" N ARG A 42 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N VAL A 36 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL A 76 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ALA A 65 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 98 through 101 Processing sheet with id= C, first strand: chain 'A' and resid 108 through 110 removed outlier: 4.123A pdb=" N ARG A 108 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ILE A 232 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N HIS A 265 " --> pdb=" O TYR A 202 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N VAL A 204 " --> pdb=" O HIS A 265 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU A 267 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL A 206 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 269 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL A 208 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ASP A 271 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N SER A 322 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE A 268 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR A 324 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N TYR A 270 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 351 through 354 removed outlier: 6.653A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU A 354 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 170 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 30 through 32 removed outlier: 6.480A pdb=" N GLY B 74 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU B 68 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLN B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N PHE B 44 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL B 33 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 98 through 101 Processing sheet with id= G, first strand: chain 'B' and resid 108 through 110 removed outlier: 4.093A pdb=" N ARG B 108 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N SER B 322 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE B 268 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR B 324 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N TYR B 270 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B 326 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 351 through 354 removed outlier: 6.534A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU B 354 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.365A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU C 68 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N PHE C 44 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL C 33 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 98 through 101 Processing sheet with id= K, first strand: chain 'C' and resid 351 through 354 removed outlier: 6.772A pdb=" N LEU C 168 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU C 354 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE C 170 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 231 through 236 removed outlier: 8.724A pdb=" N ILE C 232 " --> pdb=" O LEU C 201 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N HIS C 265 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL C 204 " --> pdb=" O HIS C 265 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU C 267 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL C 206 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL C 269 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL C 208 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASP C 271 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N SER C 322 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ILE C 268 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR C 324 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N TYR C 270 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU C 326 " --> pdb=" O TYR C 270 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 75 through 78 removed outlier: 4.930A pdb=" N ILE D 9 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 331 through 334 removed outlier: 8.296A pdb=" N ILE D 153 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER D 306 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU D 155 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLN D 308 " --> pdb=" O LEU D 155 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.549A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 331 through 334 removed outlier: 8.324A pdb=" N ILE E 153 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER E 306 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU E 155 " --> pdb=" O SER E 306 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLN E 308 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.534A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 331 through 334 removed outlier: 7.698A pdb=" N ILE F 153 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N SER F 306 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N LEU F 155 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN F 308 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N GLY F 157 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL F 310 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE F 181 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N PHE F 254 " --> pdb=" O PHE F 181 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL F 183 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ASP F 256 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR F 185 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 106 through 110 removed outlier: 4.787A pdb=" N ASN G 167 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE G 162 " --> pdb=" O ILE G 182 " (cutoff:3.500A) 975 hydrogen bonds defined for protein. 2733 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: 7.74 Time building geometry restraints manager: 9.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7814 1.34 - 1.46: 3733 1.46 - 1.58: 11859 1.58 - 1.69: 15 1.69 - 1.81: 62 Bond restraints: 23483 Sorted by residual: bond pdb=" O3 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" O4 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.568 1.507 0.061 2.00e-02 2.50e+03 9.22e+00 bond pdb=" O2 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.567 1.507 0.060 2.00e-02 2.50e+03 9.13e+00 bond pdb=" O1 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.565 1.507 0.058 2.00e-02 2.50e+03 8.34e+00 bond pdb=" N ALA G 1 " pdb=" CA ALA G 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 ... (remaining 23478 not shown) Histogram of bond angle deviations from ideal: 99.50 - 107.50: 800 107.50 - 115.50: 14548 115.50 - 123.51: 16012 123.51 - 131.51: 515 131.51 - 139.51: 17 Bond angle restraints: 31892 Sorted by residual: angle pdb=" C TYR B 339 " pdb=" N ILE B 340 " pdb=" CA ILE B 340 " ideal model delta sigma weight residual 120.24 122.61 -2.37 6.30e-01 2.52e+00 1.41e+01 angle pdb=" N GLY E 220 " pdb=" CA GLY E 220 " pdb=" C GLY E 220 " ideal model delta sigma weight residual 112.82 108.04 4.78 1.38e+00 5.25e-01 1.20e+01 angle pdb=" C ASP B 271 " pdb=" N ASP B 272 " pdb=" CA ASP B 272 " ideal model delta sigma weight residual 121.70 127.75 -6.05 1.80e+00 3.09e-01 1.13e+01 angle pdb=" C ILE B 340 " pdb=" CA ILE B 340 " pdb=" CB ILE B 340 " ideal model delta sigma weight residual 114.35 110.85 3.50 1.06e+00 8.90e-01 1.09e+01 angle pdb=" C ASP E 256 " pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta sigma weight residual 121.70 127.31 -5.61 1.80e+00 3.09e-01 9.71e+00 ... (remaining 31887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 13291 18.00 - 36.00: 745 36.00 - 53.99: 157 53.99 - 71.99: 45 71.99 - 89.99: 20 Dihedral angle restraints: 14258 sinusoidal: 5460 harmonic: 8798 Sorted by residual: dihedral pdb=" CA PHE E 219 " pdb=" C PHE E 219 " pdb=" N GLY E 220 " pdb=" CA GLY E 220 " ideal model delta harmonic sigma weight residual 180.00 152.94 27.06 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA GLU E 294 " pdb=" C GLU E 294 " pdb=" N ARG E 295 " pdb=" CA ARG E 295 " ideal model delta harmonic sigma weight residual 180.00 155.43 24.57 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA GLY F 220 " pdb=" C GLY F 220 " pdb=" N GLN F 221 " pdb=" CA GLN F 221 " ideal model delta harmonic sigma weight residual 180.00 -157.48 -22.52 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 14255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3218 0.059 - 0.119: 484 0.119 - 0.178: 76 0.178 - 0.238: 3 0.238 - 0.297: 6 Chirality restraints: 3787 Sorted by residual: chirality pdb=" C3' ATP C 600 " pdb=" C2' ATP C 600 " pdb=" C4' ATP C 600 " pdb=" O3' ATP C 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 3784 not shown) Planarity restraints: 4135 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN G 102 " -0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO G 103 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO G 103 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 103 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 173 " -0.139 9.50e-02 1.11e+02 6.24e-02 2.47e+00 pdb=" NE ARG A 173 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 173 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 173 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 173 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 470 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.89e+00 pdb=" C PHE B 470 " -0.024 2.00e-02 2.50e+03 pdb=" O PHE B 470 " 0.009 2.00e-02 2.50e+03 pdb=" N LEU B 471 " 0.008 2.00e-02 2.50e+03 ... (remaining 4132 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 114 2.57 - 3.15: 20460 3.15 - 3.74: 35039 3.74 - 4.32: 52685 4.32 - 4.90: 86747 Nonbonded interactions: 195045 Sorted by model distance: nonbonded pdb=" OG SER B 239 " pdb=" OE2 GLU E 294 " model vdw 1.991 2.440 nonbonded pdb=" O GLY D 188 " pdb=" NH1 ARG D 260 " model vdw 1.999 2.520 nonbonded pdb=" OD1 ASP C 335 " pdb=" OG SER C 337 " model vdw 2.051 2.440 nonbonded pdb=" O3G ATP A 600 " pdb="MG MG A 601 " model vdw 2.052 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 2.064 2.170 ... (remaining 195040 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 222 or (resid 223 and (name N or name CA or nam \ e C or name O or name CB )) or resid 224 through 315 or (resid 316 and (name N o \ r name CA or name C or name O or name CB )) or resid 317 through 382 or (resid 3 \ 83 through 384 and (name N or name CA or name C or name O or name CB )) or resid \ 385 through 393 or (resid 394 and (name N or name CA or name C or name O or nam \ e CB )) or resid 395 through 404 or (resid 405 through 407 and (name N or name C \ A or name C or name O or name CB )) or resid 412 through 474 or (resid 475 and ( \ name N or name CA or name C or name O or name CB )) or resid 476 through 479 or \ (resid 480 and (name N or name CA or name C or name O or name CB )) or resid 481 \ through 493 or (resid 494 and (name N or name CA or name C or name O or name CB \ )) or resid 495 through 509 or resid 600 through 601)) selection = (chain 'B' and (resid 30 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 222 or (resid 223 and (name N or n \ ame CA or name C or name O or name CB )) or resid 224 through 354 or (resid 355 \ through 357 and (name N or name CA or name C or name O or name CB )) or resid 35 \ 8 through 423 or (resid 424 and (name N or name CA or name C or name O or name C \ B )) or resid 425 through 464 or (resid 465 and (name N or name CA or name C or \ name O or name CB )) or resid 466 or (resid 467 and (name N or name CA or name C \ or name O or name CB )) or resid 468 through 474 or (resid 475 and (name N or n \ ame CA or name C or name O or name CB )) or resid 476 through 492 or (resid 493 \ through 494 and (name N or name CA or name C or name O or name CB )) or resid 49 \ 5 through 509 or resid 600 through 601)) selection = (chain 'C' and (resid 30 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 315 or (resid 316 and (name N or n \ ame CA or name C or name O or name CB )) or resid 317 through 354 or (resid 355 \ through 357 and (name N or name CA or name C or name O or name CB )) or resid 35 \ 8 through 382 or (resid 383 through 384 and (name N or name CA or name C or name \ O or name CB )) or resid 385 through 393 or (resid 394 and (name N or name CA o \ r name C or name O or name CB )) or resid 395 through 404 or (resid 405 through \ 407 and (name N or name CA or name C or name O or name CB )) or resid 412 throug \ h 423 or (resid 424 and (name N or name CA or name C or name O or name CB )) or \ resid 425 through 464 or (resid 465 and (name N or name CA or name C or name O o \ r name CB )) or resid 466 or (resid 467 and (name N or name CA or name C or name \ O or name CB )) or resid 468 through 492 or (resid 493 through 494 and (name N \ or name CA or name C or name O or name CB )) or resid 495 through 509 or resid 6 \ 00 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 27 or (resid 28 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 30 through 111 or (resid 112 and (n \ ame N or name CA or name C or name O or name CB )) or resid 113 through 168 or ( \ resid 169 and (name N or name CA or name C or name O or name CB )) or resid 170 \ through 175 or (resid 176 through 177 and (name N or name CA or name C or name O \ or name CB )) or resid 178 through 199 or (resid 200 and (name N or name CA or \ name C or name O or name CB )) or resid 201 through 299 or (resid 300 and (name \ N or name CA or name C or name O or name CB )) or resid 301 through 375 or (resi \ d 376 and (name N or name CA or name C or name O or name CB )) or resid 377 thro \ ugh 475)) selection = (chain 'E' and (resid 8 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB )) or resid 44 through 67 or (resid 68 and (name N or name \ CA or name C or name O or name CB )) or resid 69 through 104 or (resid 105 and \ (name N or name CA or name C or name O or name CB )) or resid 106 through 111 or \ (resid 112 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 3 through 168 or (resid 169 and (name N or name CA or name C or name O or name C \ B )) or resid 170 through 175 or (resid 176 through 177 and (name N or name CA o \ r name C or name O or name CB )) or resid 178 through 199 or (resid 200 and (nam \ e N or name CA or name C or name O or name CB )) or resid 201 through 209 or (re \ sid 210 and (name N or name CA or name C or name O or name CB )) or resid 211 th \ rough 383 or (resid 384 through 391 and (name N or name CA or name C or name O o \ r name CB )) or (resid 392 through 402 and (name N or name CA or name C or name \ O or name CB )) or resid 403 through 411 or (resid 412 and (name N or name CA or \ name C or name O or name CB )) or resid 413 through 434 or (resid 435 and (name \ N or name CA or name C or name O or name CB )) or resid 436 through 475)) selection = (chain 'F' and (resid 8 through 27 or (resid 28 through 29 and (name N or name C \ A or name C or name O or name CB )) or resid 30 through 42 or (resid 43 and (nam \ e N or name CA or name C or name O or name CB )) or resid 44 through 67 or (resi \ d 68 and (name N or name CA or name C or name O or name CB )) or resid 69 throug \ h 104 or (resid 105 and (name N or name CA or name C or name O or name CB )) or \ resid 106 through 299 or (resid 300 and (name N or name CA or name C or name O o \ r name CB )) or resid 301 through 314 or (resid 315 and (name N or name CA or na \ me C or name O or name CB )) or resid 316 through 375 or (resid 376 and (name N \ or name CA or name C or name O or name CB )) or resid 377 through 383 or (resid \ 384 through 391 and (name N or name CA or name C or name O or name CB )) or resi \ d 392 or (resid 393 through 402 and (name N or name CA or name C or name O or na \ me CB )) or resid 403 through 404 or (resid 405 and (name N or name CA or name C \ or name O or name CB )) or resid 406 through 411 or (resid 412 and (name N or n \ ame CA or name C or name O or name CB )) or resid 413 through 475)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.180 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 61.610 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.110 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.003 0.076 23483 Z= 0.195 Angle : 0.629 6.759 31892 Z= 0.346 Chirality : 0.046 0.297 3787 Planarity : 0.004 0.065 4135 Dihedral : 13.045 89.991 8628 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3079 helix: 0.68 (0.14), residues: 1276 sheet: 0.08 (0.23), residues: 516 loop : 0.47 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 191 HIS 0.004 0.001 HIS F 367 PHE 0.016 0.001 PHE E 243 TYR 0.014 0.002 TYR C 360 ARG 0.009 0.001 ARG E 433 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 306 time to evaluate : 3.001 Fit side-chains REVERT: A 228 MET cc_start: 0.8913 (mmm) cc_final: 0.8672 (mmt) REVERT: A 271 ASP cc_start: 0.8267 (t0) cc_final: 0.7803 (t0) REVERT: B 418 GLN cc_start: 0.7056 (tt0) cc_final: 0.6731 (tp40) REVERT: C 64 MET cc_start: 0.8426 (ttt) cc_final: 0.8185 (ttp) REVERT: C 129 SER cc_start: 0.8710 (m) cc_final: 0.8279 (p) REVERT: D 472 LYS cc_start: 0.7972 (mttm) cc_final: 0.7382 (tptt) REVERT: F 164 THR cc_start: 0.8724 (t) cc_final: 0.8288 (p) REVERT: F 172 ASN cc_start: 0.8283 (t0) cc_final: 0.8015 (t0) REVERT: F 311 TYR cc_start: 0.8746 (t80) cc_final: 0.8224 (t80) REVERT: G 113 LYS cc_start: 0.6951 (mmtt) cc_final: 0.6712 (mmtt) REVERT: G 117 GLN cc_start: 0.6598 (mm-40) cc_final: 0.6327 (mm-40) REVERT: G 222 MET cc_start: 0.7330 (ttp) cc_final: 0.7015 (ttm) REVERT: G 229 GLU cc_start: 0.7543 (tt0) cc_final: 0.7156 (tt0) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.3922 time to fit residues: 180.1432 Evaluate side-chains 209 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 239 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 277 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN D 263 GLN F 178 HIS F 328 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.094 23483 Z= 0.584 Angle : 0.717 9.514 31892 Z= 0.372 Chirality : 0.053 0.283 3787 Planarity : 0.005 0.051 4135 Dihedral : 6.977 87.801 3426 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.39 % Allowed : 5.10 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3079 helix: 0.66 (0.14), residues: 1264 sheet: -0.22 (0.22), residues: 544 loop : 0.17 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 191 HIS 0.006 0.002 HIS D 367 PHE 0.019 0.003 PHE B 506 TYR 0.028 0.002 TYR F 449 ARG 0.008 0.001 ARG A 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 218 time to evaluate : 2.508 Fit side-chains REVERT: A 271 ASP cc_start: 0.8538 (t0) cc_final: 0.8126 (t0) REVERT: A 396 LEU cc_start: 0.8977 (mp) cc_final: 0.8699 (mp) REVERT: B 418 GLN cc_start: 0.7047 (tt0) cc_final: 0.6831 (tp40) REVERT: B 422 ARG cc_start: 0.7453 (ttm170) cc_final: 0.7078 (ttm170) REVERT: C 360 TYR cc_start: 0.8073 (m-80) cc_final: 0.7780 (m-80) REVERT: D 256 ASP cc_start: 0.7867 (t0) cc_final: 0.7626 (t0) REVERT: F 64 MET cc_start: 0.8924 (mmp) cc_final: 0.8717 (mmp) REVERT: G 21 LYS cc_start: 0.8383 (mtpp) cc_final: 0.8138 (mtpp) REVERT: G 117 GLN cc_start: 0.7203 (mm-40) cc_final: 0.6675 (mm110) REVERT: G 222 MET cc_start: 0.7316 (ttp) cc_final: 0.7098 (ttm) outliers start: 33 outliers final: 30 residues processed: 237 average time/residue: 0.3882 time to fit residues: 138.8797 Evaluate side-chains 236 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 206 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain E residue 473 LEU Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 162 ILE Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 231 optimal weight: 0.1980 chunk 189 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 278 optimal weight: 0.2980 chunk 300 optimal weight: 4.9990 chunk 247 optimal weight: 0.8980 chunk 276 optimal weight: 0.4980 chunk 94 optimal weight: 8.9990 chunk 223 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 HIS D 173 ASN D 293 GLN D 308 GLN F 293 GLN F 308 GLN G 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23483 Z= 0.160 Angle : 0.502 7.590 31892 Z= 0.261 Chirality : 0.043 0.252 3787 Planarity : 0.004 0.044 4135 Dihedral : 6.336 88.990 3426 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.18 % Allowed : 6.70 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.16), residues: 3079 helix: 1.24 (0.15), residues: 1285 sheet: 0.14 (0.23), residues: 528 loop : 0.36 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 191 HIS 0.005 0.001 HIS A 478 PHE 0.016 0.001 PHE C 395 TYR 0.018 0.001 TYR F 449 ARG 0.005 0.000 ARG C 425 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 229 time to evaluate : 2.578 Fit side-chains REVERT: A 149 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7898 (mt0) REVERT: A 271 ASP cc_start: 0.8163 (t0) cc_final: 0.7957 (t0) REVERT: B 161 ILE cc_start: 0.8910 (mt) cc_final: 0.8688 (mt) REVERT: B 418 GLN cc_start: 0.6968 (tt0) cc_final: 0.6602 (tp40) REVERT: B 422 ARG cc_start: 0.7232 (ttm170) cc_final: 0.6586 (ttm170) REVERT: B 506 PHE cc_start: 0.8053 (t80) cc_final: 0.7230 (t80) REVERT: C 129 SER cc_start: 0.8711 (m) cc_final: 0.8335 (p) REVERT: D 260 ARG cc_start: 0.8479 (mmt180) cc_final: 0.8090 (mmt180) REVERT: E 41 THR cc_start: 0.7677 (OUTLIER) cc_final: 0.7124 (p) REVERT: E 368 TYR cc_start: 0.9056 (t80) cc_final: 0.8818 (t80) REVERT: G 17 GLU cc_start: 0.7261 (tm-30) cc_final: 0.7012 (tm-30) REVERT: G 21 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8206 (mtpp) REVERT: G 72 GLU cc_start: 0.4843 (tm-30) cc_final: 0.4628 (tm-30) REVERT: G 117 GLN cc_start: 0.7139 (mm-40) cc_final: 0.6722 (mm-40) outliers start: 28 outliers final: 14 residues processed: 244 average time/residue: 0.3772 time to fit residues: 140.9690 Evaluate side-chains 218 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 202 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 4.9990 chunk 209 optimal weight: 0.0670 chunk 144 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 279 optimal weight: 0.0040 chunk 295 optimal weight: 30.0000 chunk 145 optimal weight: 2.9990 chunk 264 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.8136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 HIS D 24 HIS E 24 HIS F 293 GLN G 49 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23483 Z= 0.291 Angle : 0.529 7.705 31892 Z= 0.273 Chirality : 0.045 0.259 3787 Planarity : 0.004 0.045 4135 Dihedral : 6.277 87.973 3426 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.35 % Allowed : 8.17 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.16), residues: 3079 helix: 1.32 (0.15), residues: 1279 sheet: 0.04 (0.23), residues: 532 loop : 0.31 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 191 HIS 0.004 0.001 HIS A 478 PHE 0.013 0.001 PHE B 506 TYR 0.022 0.001 TYR F 449 ARG 0.004 0.000 ARG C 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 215 time to evaluate : 2.811 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: B 161 ILE cc_start: 0.8936 (mt) cc_final: 0.8734 (mt) REVERT: B 418 GLN cc_start: 0.7036 (tt0) cc_final: 0.6646 (tp40) REVERT: B 422 ARG cc_start: 0.7169 (ttm170) cc_final: 0.6550 (ttm170) REVERT: C 129 SER cc_start: 0.8720 (m) cc_final: 0.8330 (p) REVERT: D 249 GLN cc_start: 0.8234 (mt0) cc_final: 0.7768 (mm-40) REVERT: E 41 THR cc_start: 0.7652 (OUTLIER) cc_final: 0.7178 (p) REVERT: E 241 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6904 (mt-10) REVERT: F 293 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8213 (mm-40) REVERT: G 17 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6993 (tm-30) REVERT: G 21 LYS cc_start: 0.8411 (mtpp) cc_final: 0.8156 (mtpp) outliers start: 32 outliers final: 22 residues processed: 235 average time/residue: 0.3701 time to fit residues: 132.7472 Evaluate side-chains 232 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 207 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 220 optimal weight: 0.0870 chunk 122 optimal weight: 0.0870 chunk 252 optimal weight: 6.9990 chunk 204 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 265 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 overall best weight: 0.9738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS C 478 HIS E 221 GLN G 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23483 Z= 0.189 Angle : 0.484 7.677 31892 Z= 0.250 Chirality : 0.043 0.277 3787 Planarity : 0.003 0.044 4135 Dihedral : 6.052 88.035 3426 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.18 % Allowed : 8.89 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.16), residues: 3079 helix: 1.52 (0.15), residues: 1283 sheet: 0.14 (0.23), residues: 529 loop : 0.40 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 191 HIS 0.005 0.001 HIS A 478 PHE 0.011 0.001 PHE F 261 TYR 0.019 0.001 TYR F 449 ARG 0.004 0.000 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 219 time to evaluate : 3.029 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7897 (mt0) REVERT: B 161 ILE cc_start: 0.8930 (mt) cc_final: 0.8728 (mt) REVERT: B 392 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7900 (tp) REVERT: C 129 SER cc_start: 0.8707 (m) cc_final: 0.8317 (p) REVERT: D 249 GLN cc_start: 0.8233 (mt0) cc_final: 0.7808 (mm-40) REVERT: D 260 ARG cc_start: 0.8585 (mmt180) cc_final: 0.8290 (mmt180) REVERT: E 41 THR cc_start: 0.7635 (OUTLIER) cc_final: 0.7192 (p) REVERT: G 17 GLU cc_start: 0.7358 (tm-30) cc_final: 0.7032 (tm-30) REVERT: G 117 GLN cc_start: 0.6330 (mm-40) cc_final: 0.6059 (mm-40) REVERT: G 180 LYS cc_start: 0.7855 (mtpp) cc_final: 0.7619 (mtmt) outliers start: 28 outliers final: 19 residues processed: 240 average time/residue: 0.3845 time to fit residues: 141.2565 Evaluate side-chains 227 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 205 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 173 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 296 optimal weight: 1.9990 chunk 245 optimal weight: 0.0870 chunk 137 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 478 HIS G 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23483 Z= 0.252 Angle : 0.498 7.731 31892 Z= 0.256 Chirality : 0.044 0.303 3787 Planarity : 0.004 0.045 4135 Dihedral : 6.021 88.234 3426 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.43 % Allowed : 9.27 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.16), residues: 3079 helix: 1.51 (0.15), residues: 1282 sheet: 0.07 (0.23), residues: 529 loop : 0.38 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 191 HIS 0.005 0.001 HIS A 478 PHE 0.012 0.001 PHE B 506 TYR 0.018 0.001 TYR F 449 ARG 0.003 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 2.809 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7909 (mt0) REVERT: C 129 SER cc_start: 0.8724 (m) cc_final: 0.8342 (p) REVERT: C 496 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8722 (mt) REVERT: D 249 GLN cc_start: 0.8304 (mt0) cc_final: 0.7853 (mm-40) REVERT: D 260 ARG cc_start: 0.8609 (mmt180) cc_final: 0.8310 (mmt180) REVERT: E 41 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7252 (p) REVERT: E 241 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6906 (mt-10) REVERT: G 17 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7090 (tm-30) REVERT: G 21 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7946 (mtpp) REVERT: G 117 GLN cc_start: 0.6266 (mm-40) cc_final: 0.5999 (mm-40) REVERT: G 180 LYS cc_start: 0.7898 (mtpp) cc_final: 0.7677 (mtmt) outliers start: 34 outliers final: 22 residues processed: 232 average time/residue: 0.4016 time to fit residues: 144.8769 Evaluate side-chains 228 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 203 time to evaluate : 2.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 216 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 chunk 249 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 294 optimal weight: 30.0000 chunk 184 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23483 Z= 0.332 Angle : 0.532 7.797 31892 Z= 0.274 Chirality : 0.045 0.327 3787 Planarity : 0.004 0.045 4135 Dihedral : 6.154 88.848 3426 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.64 % Allowed : 9.86 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.16), residues: 3079 helix: 1.49 (0.15), residues: 1267 sheet: -0.08 (0.23), residues: 534 loop : 0.31 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 191 HIS 0.006 0.001 HIS A 478 PHE 0.018 0.001 PHE B 466 TYR 0.019 0.001 TYR F 449 ARG 0.003 0.000 ARG C 425 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 207 time to evaluate : 2.743 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.7899 (mt0) REVERT: C 129 SER cc_start: 0.8672 (m) cc_final: 0.8274 (p) REVERT: C 496 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8752 (mt) REVERT: D 249 GLN cc_start: 0.8239 (mt0) cc_final: 0.7842 (mm-40) REVERT: D 260 ARG cc_start: 0.8631 (mmt180) cc_final: 0.8310 (mmt180) REVERT: E 41 THR cc_start: 0.7648 (OUTLIER) cc_final: 0.7276 (p) REVERT: E 241 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6957 (mt-10) REVERT: G 17 GLU cc_start: 0.7301 (tm-30) cc_final: 0.7070 (tm-30) REVERT: G 21 LYS cc_start: 0.8170 (mtpp) cc_final: 0.7948 (mtpp) REVERT: G 117 GLN cc_start: 0.6260 (mm-40) cc_final: 0.6005 (mm-40) REVERT: G 180 LYS cc_start: 0.7897 (mtpp) cc_final: 0.7361 (mmmt) outliers start: 39 outliers final: 27 residues processed: 234 average time/residue: 0.3649 time to fit residues: 132.3709 Evaluate side-chains 233 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 203 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 163 LYS Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 218 MET Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 57 optimal weight: 0.4980 chunk 187 optimal weight: 9.9990 chunk 200 optimal weight: 0.0040 chunk 145 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 231 optimal weight: 0.0070 chunk 268 optimal weight: 0.9990 overall best weight: 0.3810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 ASN G 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23483 Z= 0.136 Angle : 0.458 7.613 31892 Z= 0.236 Chirality : 0.042 0.321 3787 Planarity : 0.003 0.045 4135 Dihedral : 5.744 89.946 3426 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.14 % Allowed : 10.61 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.16), residues: 3079 helix: 1.70 (0.15), residues: 1283 sheet: 0.12 (0.23), residues: 526 loop : 0.45 (0.18), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 191 HIS 0.005 0.001 HIS A 478 PHE 0.013 0.001 PHE B 466 TYR 0.018 0.001 TYR B 473 ARG 0.004 0.000 ARG B 425 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 222 time to evaluate : 2.797 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7833 (mt0) REVERT: B 67 ASN cc_start: 0.8250 (m-40) cc_final: 0.8017 (m110) REVERT: C 129 SER cc_start: 0.8660 (m) cc_final: 0.8246 (p) REVERT: C 496 LEU cc_start: 0.9072 (mt) cc_final: 0.8718 (mt) REVERT: D 249 GLN cc_start: 0.8160 (mt0) cc_final: 0.7644 (mm-40) REVERT: D 260 ARG cc_start: 0.8556 (mmt180) cc_final: 0.8215 (mmt180) REVERT: F 256 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6901 (t70) REVERT: F 449 TYR cc_start: 0.8613 (m-80) cc_final: 0.8337 (m-80) REVERT: G 17 GLU cc_start: 0.7339 (tm-30) cc_final: 0.7035 (tm-30) REVERT: G 21 LYS cc_start: 0.8120 (mtpp) cc_final: 0.7874 (mtpp) outliers start: 27 outliers final: 17 residues processed: 240 average time/residue: 0.3744 time to fit residues: 137.9694 Evaluate side-chains 223 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 chunk 274 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 215 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 259 optimal weight: 0.5980 chunk 273 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23483 Z= 0.171 Angle : 0.464 7.660 31892 Z= 0.237 Chirality : 0.042 0.345 3787 Planarity : 0.003 0.043 4135 Dihedral : 5.642 89.890 3426 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.01 % Allowed : 11.20 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.16), residues: 3079 helix: 1.80 (0.15), residues: 1279 sheet: 0.16 (0.23), residues: 517 loop : 0.49 (0.18), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 191 HIS 0.006 0.001 HIS A 478 PHE 0.013 0.001 PHE B 466 TYR 0.019 0.001 TYR F 449 ARG 0.004 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 2.744 Fit side-chains revert: symmetry clash REVERT: A 149 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7826 (mt0) REVERT: B 67 ASN cc_start: 0.8254 (m-40) cc_final: 0.8018 (m110) REVERT: B 267 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8267 (tp) REVERT: C 129 SER cc_start: 0.8660 (m) cc_final: 0.8231 (p) REVERT: C 496 LEU cc_start: 0.9070 (mt) cc_final: 0.8733 (mt) REVERT: D 249 GLN cc_start: 0.8066 (mt0) cc_final: 0.7653 (mm-40) REVERT: D 260 ARG cc_start: 0.8578 (mmt180) cc_final: 0.8253 (mmt180) REVERT: F 256 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6950 (t70) REVERT: G 17 GLU cc_start: 0.7330 (tm-30) cc_final: 0.7005 (tm-30) REVERT: G 180 LYS cc_start: 0.7987 (mtmt) cc_final: 0.7389 (mmmt) outliers start: 24 outliers final: 18 residues processed: 227 average time/residue: 0.3753 time to fit residues: 132.3562 Evaluate side-chains 226 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 205 time to evaluate : 2.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 20.0000 chunk 177 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 304 optimal weight: 5.9990 chunk 280 optimal weight: 0.8980 chunk 242 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 192 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23483 Z= 0.252 Angle : 0.498 7.733 31892 Z= 0.254 Chirality : 0.044 0.351 3787 Planarity : 0.004 0.043 4135 Dihedral : 5.744 89.651 3426 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.10 % Allowed : 11.46 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.16), residues: 3079 helix: 1.71 (0.15), residues: 1278 sheet: 0.11 (0.23), residues: 515 loop : 0.43 (0.18), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 191 HIS 0.006 0.001 HIS A 478 PHE 0.012 0.001 PHE B 466 TYR 0.014 0.001 TYR B 448 ARG 0.004 0.000 ARG A 375 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 203 time to evaluate : 2.774 Fit side-chains REVERT: A 149 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7899 (mt0) REVERT: B 67 ASN cc_start: 0.8262 (m-40) cc_final: 0.8031 (m110) REVERT: B 267 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8281 (tp) REVERT: C 129 SER cc_start: 0.8656 (m) cc_final: 0.8231 (p) REVERT: C 496 LEU cc_start: 0.9089 (mt) cc_final: 0.8748 (mt) REVERT: D 249 GLN cc_start: 0.8084 (mt0) cc_final: 0.7650 (mm-40) REVERT: D 260 ARG cc_start: 0.8599 (mmt180) cc_final: 0.8304 (mmt180) REVERT: F 256 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.7049 (t70) REVERT: G 17 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7128 (tm-30) outliers start: 26 outliers final: 22 residues processed: 220 average time/residue: 0.3718 time to fit residues: 126.2267 Evaluate side-chains 222 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 GLN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 467 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 305 THR Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 336 SER Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 460 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 256 ASP Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 246 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 2.9990 chunk 74 optimal weight: 0.0020 chunk 223 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 243 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.134156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.106518 restraints weight = 28857.031| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.57 r_work: 0.3050 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23483 Z= 0.182 Angle : 0.477 7.658 31892 Z= 0.242 Chirality : 0.043 0.333 3787 Planarity : 0.003 0.044 4135 Dihedral : 5.636 89.701 3426 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.14 % Allowed : 11.67 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.16), residues: 3079 helix: 1.80 (0.15), residues: 1277 sheet: 0.17 (0.23), residues: 515 loop : 0.45 (0.18), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 191 HIS 0.006 0.001 HIS A 478 PHE 0.013 0.001 PHE B 395 TYR 0.015 0.001 TYR F 449 ARG 0.004 0.000 ARG B 425 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4535.38 seconds wall clock time: 83 minutes 29.71 seconds (5009.71 seconds total)