Starting phenix.real_space_refine (version: dev) on Fri Feb 24 13:20:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjt_25931/02_2023/7tjt_25931_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjt_25931/02_2023/7tjt_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_2023/7tjt_25931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjt_25931/02_2023/7tjt_25931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjt_25931/02_2023/7tjt_25931_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjt_25931/02_2023/7tjt_25931_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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 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-4877/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: 12.38, per 1000 atoms: 0.54 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: 9.24 Conformation dependent library (CDL) restraints added in 3.6 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: 2.72 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: 8.30 Time building geometry restraints manager: 9.89 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 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 TYR C 339 " pdb=" N ILE C 340 " pdb=" CA ILE C 340 " ideal model delta sigma weight residual 120.33 122.76 -2.43 8.00e-01 1.56e+00 9.25e+00 angle pdb=" N ILE F 344 " pdb=" CA ILE F 344 " pdb=" C ILE F 344 " ideal model delta sigma weight residual 106.21 109.11 -2.90 1.07e+00 8.73e-01 7.34e+00 ... (remaining 31887 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 13251 18.00 - 36.00: 720 36.00 - 53.99: 137 53.99 - 71.99: 39 71.99 - 89.99: 18 Dihedral angle restraints: 14165 sinusoidal: 5367 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 14162 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 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. 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: 0.780 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: 5.890 Check model and map are aligned: 0.320 Process input model: 59.580 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.420 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 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 : 0.628 6.759 31892 Z= 0.344 Chirality : 0.046 0.297 3787 Planarity : 0.004 0.065 4135 Dihedral : 12.675 89.991 8535 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 % 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 *********************** 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 : 2.727 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.3968 time to fit residues: 182.2138 Evaluate side-chains 208 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 2.682 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.5965 ------------------------------------------------------------------------------- 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: 0.8558 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.093 23483 Z= 0.583 Angle : 0.719 10.017 31892 Z= 0.370 Chirality : 0.052 0.284 3787 Planarity : 0.005 0.048 4135 Dihedral : 5.510 79.757 3333 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 1.39 % 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: 0.37 (0.15), residues: 3079 helix: 0.69 (0.14), residues: 1263 sheet: -0.18 (0.22), residues: 555 loop : 0.21 (0.18), residues: 1261 *********************** 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 253 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 220 time to evaluate : 2.964 Fit side-chains outliers start: 33 outliers final: 30 residues processed: 239 average time/residue: 0.3993 time to fit residues: 144.7836 Evaluate side-chains 232 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 202 time to evaluate : 2.804 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2206 time to fit residues: 16.0349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 278 optimal weight: 0.5980 chunk 300 optimal weight: 9.9990 chunk 247 optimal weight: 1.9990 chunk 276 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 chunk 223 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 304 HIS C 478 HIS D 173 ASN D 293 GLN D 308 GLN ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 23483 Z= 0.204 Angle : 0.525 7.888 31892 Z= 0.271 Chirality : 0.044 0.246 3787 Planarity : 0.004 0.045 4135 Dihedral : 4.996 72.874 3333 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 0.59 % 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: 0.82 (0.16), residues: 3079 helix: 1.14 (0.15), residues: 1283 sheet: 0.00 (0.22), residues: 549 loop : 0.36 (0.19), residues: 1247 *********************** 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 241 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 227 time to evaluate : 2.983 Fit side-chains outliers start: 14 outliers final: 4 residues processed: 239 average time/residue: 0.3962 time to fit residues: 144.5374 Evaluate side-chains 203 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 199 time to evaluate : 2.768 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2746 time to fit residues: 5.8281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1980 chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 279 optimal weight: 2.9990 chunk 295 optimal weight: 30.0000 chunk 145 optimal weight: 4.9990 chunk 264 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN C 478 HIS D 24 HIS E 24 HIS ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 23483 Z= 0.275 Angle : 0.530 7.711 31892 Z= 0.272 Chirality : 0.045 0.272 3787 Planarity : 0.004 0.045 4135 Dihedral : 4.805 66.620 3333 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 0.93 % 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: 0.90 (0.16), residues: 3079 helix: 1.31 (0.15), residues: 1279 sheet: -0.01 (0.23), residues: 530 loop : 0.30 (0.18), residues: 1270 *********************** 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 234 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 212 time to evaluate : 2.890 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 224 average time/residue: 0.4063 time to fit residues: 139.1701 Evaluate side-chains 216 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 201 time to evaluate : 2.988 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2148 time to fit residues: 10.0751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 0.1980 chunk 167 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 220 optimal weight: 2.9990 chunk 122 optimal weight: 0.0980 chunk 252 optimal weight: 7.9990 chunk 204 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 151 optimal weight: 0.0770 chunk 265 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS A 434 GLN C 478 HIS ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN F 293 GLN F 308 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 23483 Z= 0.141 Angle : 0.475 7.609 31892 Z= 0.243 Chirality : 0.042 0.275 3787 Planarity : 0.003 0.044 4135 Dihedral : 4.491 60.808 3333 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 0.51 % 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: 1.18 (0.16), residues: 3079 helix: 1.53 (0.15), residues: 1288 sheet: 0.18 (0.23), residues: 516 loop : 0.43 (0.18), residues: 1275 *********************** 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 233 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 221 time to evaluate : 2.655 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 229 average time/residue: 0.4047 time to fit residues: 140.8843 Evaluate side-chains 205 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 203 time to evaluate : 2.785 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2277 time to fit residues: 4.5623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 0.9980 chunk 266 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 173 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 296 optimal weight: 20.0000 chunk 245 optimal weight: 0.0370 chunk 137 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 97 optimal weight: 0.2980 chunk 155 optimal weight: 7.9990 overall best weight: 1.2660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN D 249 GLN G 49 GLN G 217 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2140 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= 0.222 Angle : 0.492 7.708 31892 Z= 0.250 Chirality : 0.043 0.319 3787 Planarity : 0.004 0.042 4135 Dihedral : 4.422 57.281 3333 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer Outliers : 0.67 % 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: 1.22 (0.16), residues: 3079 helix: 1.59 (0.15), residues: 1285 sheet: 0.15 (0.23), residues: 512 loop : 0.45 (0.18), residues: 1282 *********************** 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 223 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 207 time to evaluate : 2.874 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 215 average time/residue: 0.3961 time to fit residues: 130.8950 Evaluate side-chains 209 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 199 time to evaluate : 2.759 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2165 time to fit residues: 7.8074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 249 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 294 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 23483 Z= 0.336 Angle : 0.540 8.202 31892 Z= 0.274 Chirality : 0.045 0.345 3787 Planarity : 0.004 0.044 4135 Dihedral : 4.565 54.401 3333 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.63 % 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: 1.05 (0.16), residues: 3079 helix: 1.51 (0.15), residues: 1268 sheet: -0.02 (0.23), residues: 534 loop : 0.36 (0.18), residues: 1277 *********************** 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 218 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 203 time to evaluate : 2.802 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 213 average time/residue: 0.3889 time to fit residues: 127.5488 Evaluate side-chains 201 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 198 time to evaluate : 3.012 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2197 time to fit residues: 4.9800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 176 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 200 optimal weight: 0.1980 chunk 145 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 231 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN C 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 23483 Z= 0.202 Angle : 0.487 7.696 31892 Z= 0.247 Chirality : 0.043 0.322 3787 Planarity : 0.003 0.045 4135 Dihedral : 4.399 51.617 3333 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer Outliers : 0.42 % 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: 1.17 (0.16), residues: 3079 helix: 1.58 (0.15), residues: 1284 sheet: 0.07 (0.23), residues: 518 loop : 0.40 (0.18), residues: 1277 *********************** 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 224 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 214 time to evaluate : 2.811 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 220 average time/residue: 0.3935 time to fit residues: 134.3816 Evaluate side-chains 203 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 200 time to evaluate : 2.859 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3233 time to fit residues: 5.6719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 165 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 259 optimal weight: 0.9990 chunk 273 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN B 67 ASN G 98 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2395 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= 0.180 Angle : 0.476 7.681 31892 Z= 0.241 Chirality : 0.043 0.341 3787 Planarity : 0.003 0.044 4135 Dihedral : 4.271 49.766 3333 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer Outliers : 0.34 % 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: 1.29 (0.16), residues: 3079 helix: 1.69 (0.15), residues: 1281 sheet: 0.16 (0.23), residues: 516 loop : 0.46 (0.18), residues: 1282 *********************** 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 214 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 206 time to evaluate : 3.033 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 211 average time/residue: 0.4102 time to fit residues: 132.8137 Evaluate side-chains 199 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 196 time to evaluate : 2.799 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2145 time to fit residues: 5.0045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 8.9990 chunk 177 optimal weight: 0.8980 chunk 137 optimal weight: 0.2980 chunk 202 optimal weight: 2.9990 chunk 304 optimal weight: 5.9990 chunk 280 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 192 optimal weight: 5.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 249 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 23483 Z= 0.389 Angle : 0.558 8.364 31892 Z= 0.283 Chirality : 0.046 0.357 3787 Planarity : 0.004 0.044 4135 Dihedral : 4.516 50.743 3333 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.17 % 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: 1.03 (0.16), residues: 3079 helix: 1.49 (0.15), residues: 1275 sheet: -0.01 (0.24), residues: 514 loop : 0.31 (0.18), residues: 1290 ********************** 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 208 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 204 time to evaluate : 2.815 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 205 average time/residue: 0.4184 time to fit residues: 134.3228 Evaluate side-chains 199 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 2.757 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2110 time to fit residues: 4.1345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 0.7980 chunk 74 optimal weight: 0.0370 chunk 223 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 249 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 213 optimal weight: 1.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 249 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.134815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.106940 restraints weight = 28782.307| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.52 r_work: 0.3023 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 23483 Z= 0.169 Angle : 0.484 8.032 31892 Z= 0.245 Chirality : 0.043 0.340 3787 Planarity : 0.003 0.044 4135 Dihedral : 4.281 47.564 3333 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 0.04 % 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: 1.23 (0.16), residues: 3079 helix: 1.64 (0.15), residues: 1288 sheet: 0.10 (0.23), residues: 520 loop : 0.42 (0.18), residues: 1271 =============================================================================== Job complete usr+sys time: 4333.80 seconds wall clock time: 79 minutes 51.06 seconds (4791.06 seconds total)