Starting phenix.real_space_refine on Tue Mar 19 01:37:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tju_25932/03_2024/7tju_25932_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tju_25932/03_2024/7tju_25932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tju_25932/03_2024/7tju_25932.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tju_25932/03_2024/7tju_25932.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tju_25932/03_2024/7tju_25932_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tju_25932/03_2024/7tju_25932_updated.pdb" } resolution = 3.3 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= 0.223 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 29 5.16 5 C 14301 2.51 5 N 3993 2.21 5 O 4351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22687 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3555 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 461} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 72 Chain: "B" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3517 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 457} Chain breaks: 1 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 3616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3616 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 461} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3437 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 56 Chain: "E" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3486 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 42 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3524 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 444} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1451 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 561 Unresolved non-hydrogen angles: 698 Unresolved non-hydrogen dihedrals: 467 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 13, 'ASP:plan': 11, 'PHE:plan': 8, 'GLU:plan': 12, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 273 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: 12.32, per 1000 atoms: 0.54 Number of scatterers: 22687 At special positions: 0 Unit cell: (126.828, 128.135, 149.055, 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 29 16.00 P 10 15.00 Mg 3 11.99 O 4351 8.00 N 3993 7.00 C 14301 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: 9.36 Conformation dependent library (CDL) restraints added in 4.7 seconds 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5636 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 131 helices and 22 sheets defined 44.7% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.61 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 removed outlier: 3.506A pdb=" N ALA A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.834A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 5.131A 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 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 261 Proline residue: A 249 - end of helix removed outlier: 3.564A pdb=" N TRP A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.892A 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: 3.501A pdb=" N ARG A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.611A 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 339 through 347 Processing helix chain 'A' and resid 356 through 359 No H-bonds generated for 'chain 'A' and resid 356 through 359' 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 406 removed outlier: 3.984A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 3.630A pdb=" N LEU A 429 " --> pdb=" O ARG A 425 " (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 Processing helix chain 'A' and resid 460 through 477 removed outlier: 5.539A pdb=" N GLY A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER A 468 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 470 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN A 477 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 Processing helix chain 'A' and resid 493 through 508 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: 3.952A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.990A 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 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 242 through 261 Proline residue: B 249 - end of helix removed outlier: 3.619A pdb=" N TRP B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 3.959A 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 300 through 310 removed outlier: 3.563A pdb=" N ARG B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG B 310 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' 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 392 through 405 removed outlier: 3.538A pdb=" N GLU B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 430 removed outlier: 3.577A pdb=" N ARG B 425 " --> pdb=" O VAL B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 452 Proline residue: B 445 - end of helix Processing helix chain 'B' and resid 454 through 457 removed outlier: 4.116A 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: 4.471A pdb=" N GLY B 464 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU B 467 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU B 471 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS B 475 " --> pdb=" O SER B 472 " (cutoff:3.500A) removed outlier: 3.680A 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 507 removed outlier: 3.627A pdb=" N THR B 503 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 83 No H-bonds generated for 'chain 'C' and resid 81 through 83' 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 removed outlier: 3.609A pdb=" N LEU C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.882A pdb=" N GLN C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 5.201A 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 227 through 230 removed outlier: 3.705A pdb=" N TYR C 230 " --> pdb=" O ALA C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 242 through 261 Proline residue: C 249 - end of helix removed outlier: 3.525A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 4.044A 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: 4.612A pdb=" N ARG C 310 " --> pdb=" O ARG C 306 " (cutoff:3.500A) 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 390 removed outlier: 3.605A pdb=" N GLY C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 408 removed outlier: 3.650A pdb=" N GLU C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 408 " --> pdb=" O ALA C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 429 removed outlier: 3.787A pdb=" N THR C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 3.643A 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 454 through 457 removed outlier: 4.027A pdb=" N GLY C 457 " --> pdb=" O HIS C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 454 through 457' Processing helix chain 'C' and resid 460 through 477 removed outlier: 4.371A pdb=" N GLY C 464 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU C 467 " --> pdb=" O GLY C 464 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE C 470 " --> pdb=" O GLU C 467 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU C 471 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS C 475 " --> pdb=" O SER C 472 " (cutoff:3.500A) removed outlier: 3.600A 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 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: 4.755A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 272 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 283 through 296 removed outlier: 4.451A pdb=" N ALA D 286 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLU D 294 " --> 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: 3.516A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N HIS D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 341 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: 3.842A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (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: 3.622A pdb=" N LYS D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 425 removed outlier: 4.214A pdb=" N VAL D 423 " --> pdb=" O VAL D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 445 Processing helix chain 'D' and resid 454 through 457 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 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 139 through 144 Processing helix chain 'E' and resid 163 through 178 Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 226 through 247 removed outlier: 5.191A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE E 243 " --> pdb=" O ILE E 239 " (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 296 removed outlier: 4.621A pdb=" N ARG E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE E 296 " --> pdb=" O LEU E 292 " (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: 4.231A 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 390 removed outlier: 4.107A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) removed outlier: 4.165A 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 420 through 423 removed outlier: 3.969A pdb=" N VAL E 423 " --> pdb=" O VAL E 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 420 through 423' 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 474 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 139 through 144 Processing helix chain 'F' and resid 163 through 178 removed outlier: 4.655A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 226 through 245 removed outlier: 4.623A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 272 removed outlier: 3.614A pdb=" N VAL F 268 " --> pdb=" O GLY F 265 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA F 270 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 295 removed outlier: 4.418A pdb=" N ALA F 286 " --> pdb=" O PRO F 283 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU F 291 " --> pdb=" O ASP F 288 " (cutoff:3.500A) removed outlier: 4.618A 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 327 removed outlier: 4.259A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 342 removed outlier: 4.056A pdb=" N LEU F 342 " --> pdb=" O GLY F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 363 No H-bonds generated for 'chain 'F' and resid 360 through 363' Processing helix chain 'F' and resid 365 through 391 removed outlier: 4.883A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) 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 413 Processing helix chain 'F' and resid 419 through 425 removed outlier: 4.023A pdb=" N VAL F 423 " --> pdb=" O VAL F 420 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR F 425 " --> pdb=" O GLU F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 446 Processing helix chain 'F' and resid 454 through 457 Processing helix chain 'F' and resid 463 through 474 Processing helix chain 'G' and resid 3 through 55 removed outlier: 4.384A pdb=" N SER G 32 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU G 46 " --> pdb=" O LYS G 42 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ALA G 47 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU G 48 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 102 removed outlier: 3.648A pdb=" N ALA G 92 " --> pdb=" O HIS G 88 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASP G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLN G 102 " --> pdb=" O HIS G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 120 removed outlier: 4.080A pdb=" N LEU G 119 " --> pdb=" O LYS G 115 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG G 120 " --> pdb=" O MET G 116 " (cutoff:3.500A) 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 133 through 135 No H-bonds generated for 'chain 'G' and resid 133 through 135' Processing helix chain 'G' and resid 140 through 154 removed outlier: 4.173A pdb=" N LEU G 145 " --> pdb=" O GLN G 141 " (cutoff:3.500A) 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 189 removed outlier: 3.667A pdb=" N GLU G 189 " --> pdb=" O LYS G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 196 removed outlier: 3.850A pdb=" N GLY G 195 " --> pdb=" O PRO G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 275 removed outlier: 3.941A pdb=" N LEU G 214 " --> pdb=" O PHE G 210 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP G 238 " --> pdb=" O ARG G 234 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY G 245 " --> pdb=" O SER G 241 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET G 247 " --> pdb=" O ASN G 243 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.508A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU A 68 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLN A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N PHE A 44 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL A 33 " --> pdb=" O PHE A 44 " (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 351 through 354 removed outlier: 6.491A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU A 354 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE A 170 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 231 through 236 removed outlier: 6.639A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N SER A 322 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ILE A 268 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR A 324 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N TYR A 270 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 30 through 32 removed outlier: 7.023A pdb=" N GLY B 74 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU B 68 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLN B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE B 44 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.432A 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 351 through 354 removed outlier: 6.354A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU B 354 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 231 through 236 removed outlier: 6.485A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER B 322 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE B 268 " --> pdb=" O SER B 322 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR B 324 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N TYR B 270 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 326 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.591A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LEU C 68 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLN C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE C 44 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.489A 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 108 through 110 removed outlier: 4.096A pdb=" N ARG C 108 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N SER C 322 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE C 268 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR C 324 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N TYR C 270 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU C 326 " --> pdb=" O TYR C 270 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 351 through 354 removed outlier: 6.592A pdb=" N LEU C 168 " --> pdb=" O ILE C 352 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU C 354 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE C 170 " --> pdb=" O LEU C 354 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.585A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.639A 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: 8.278A pdb=" N ILE D 153 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER D 306 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU D 155 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.332A 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: 6.577A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.571A 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: 8.385A pdb=" N ILE E 153 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SER E 306 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU E 155 " --> pdb=" O SER E 306 " (cutoff:3.500A) removed outlier: 6.330A 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: 6.556A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.615A 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: 7.642A pdb=" N ILE F 153 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N SER F 306 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU F 155 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN F 308 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N GLY F 157 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL F 310 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL F 251 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL F 307 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU F 253 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA F 309 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE F 255 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N TYR F 311 " --> pdb=" O ILE F 255 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 176 through 182 removed outlier: 6.603A pdb=" N LEU G 73 " --> pdb=" O SER G 163 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N PHE G 165 " --> pdb=" O LEU G 73 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL G 75 " --> pdb=" O PHE G 165 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N ASN G 167 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ILE G 77 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASP G 106 " --> pdb=" O ILE G 74 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ALA G 76 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL G 108 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N THR G 109 " --> pdb=" O LYS G 127 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER G 129 " --> pdb=" O THR G 109 " (cutoff:3.500A) 986 hydrogen bonds defined for protein. 2700 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: 7.69 Time building geometry restraints manager: 10.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7731 1.34 - 1.46: 3828 1.46 - 1.58: 11387 1.58 - 1.69: 15 1.69 - 1.81: 55 Bond restraints: 23016 Sorted by residual: 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 9.27e+00 bond pdb=" O3 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" O2 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.74e+00 bond pdb=" O1 PO4 F 600 " pdb=" P PO4 F 600 " ideal model delta sigma weight residual 1.565 1.508 0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" N ALA G 1 " pdb=" CA ALA G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 ... (remaining 23011 not shown) Histogram of bond angle deviations from ideal: 99.56 - 107.64: 783 107.64 - 115.71: 14424 115.71 - 123.79: 15668 123.79 - 131.87: 400 131.87 - 139.95: 15 Bond angle restraints: 31290 Sorted by residual: angle pdb=" C ALA F 278 " pdb=" CA ALA F 278 " pdb=" CB ALA F 278 " ideal model delta sigma weight residual 116.54 111.24 5.30 1.15e+00 7.56e-01 2.13e+01 angle pdb=" C TYR A 339 " pdb=" N ILE A 340 " pdb=" CA ILE A 340 " ideal model delta sigma weight residual 120.24 122.70 -2.46 6.30e-01 2.52e+00 1.53e+01 angle pdb=" C ILE A 340 " pdb=" CA ILE A 340 " pdb=" CB ILE A 340 " ideal model delta sigma weight residual 114.35 110.88 3.47 1.06e+00 8.90e-01 1.07e+01 angle pdb=" C ASP E 256 " pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta sigma weight residual 121.70 127.52 -5.82 1.80e+00 3.09e-01 1.05e+01 angle pdb=" N VAL G 205 " pdb=" CA VAL G 205 " pdb=" C VAL G 205 " ideal model delta sigma weight residual 112.61 108.03 4.58 1.45e+00 4.76e-01 9.98e+00 ... (remaining 31285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13171 17.93 - 35.85: 572 35.85 - 53.78: 133 53.78 - 71.70: 45 71.70 - 89.63: 27 Dihedral angle restraints: 13948 sinusoidal: 5147 harmonic: 8801 Sorted by residual: dihedral pdb=" CA GLY E 220 " pdb=" C GLY E 220 " pdb=" N GLN E 221 " pdb=" CA GLN E 221 " ideal model delta harmonic sigma weight residual -180.00 -157.39 -22.61 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ARG D 274 " pdb=" C ARG D 274 " pdb=" N ILE D 275 " pdb=" CA ILE D 275 " ideal model delta harmonic sigma weight residual -180.00 -157.64 -22.36 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA ILE D 103 " pdb=" C ILE D 103 " pdb=" N ASP D 104 " pdb=" CA ASP D 104 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 13945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3172 0.059 - 0.119: 482 0.119 - 0.178: 81 0.178 - 0.237: 2 0.237 - 0.296: 7 Chirality restraints: 3744 Sorted by residual: chirality pdb=" C2' ATP C 600 " pdb=" C1' ATP C 600 " pdb=" C3' ATP C 600 " pdb=" O2' ATP C 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.20e+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 2.15e+00 chirality pdb=" C3' ATP B 600 " pdb=" C2' ATP B 600 " pdb=" C4' ATP B 600 " pdb=" O3' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 3741 not shown) Planarity restraints: 4073 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 473 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C TYR B 473 " 0.028 2.00e-02 2.50e+03 pdb=" O TYR B 473 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU B 474 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 406 " 0.120 9.50e-02 1.11e+02 5.44e-02 2.47e+00 pdb=" NE ARG E 406 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG E 406 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG E 406 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG E 406 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 146 " -0.025 5.00e-02 4.00e+02 3.70e-02 2.20e+00 pdb=" N PRO B 147 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 147 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 147 " -0.021 5.00e-02 4.00e+02 ... (remaining 4070 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 195 2.64 - 3.20: 22146 3.20 - 3.77: 34195 3.77 - 4.33: 50728 4.33 - 4.90: 82334 Nonbonded interactions: 189598 Sorted by model distance: nonbonded pdb=" OG1 THR A 178 " pdb="MG MG A 601 " model vdw 2.070 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 2.070 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 2.071 2.170 nonbonded pdb=" OG1 THR B 178 " pdb="MG MG B 601 " model vdw 2.079 2.170 nonbonded pdb=" OG1 THR C 178 " pdb="MG MG C 601 " model vdw 2.079 2.170 ... (remaining 189593 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 28 through 29 and (name N or name CA or name C or name O \ or name CB )) or resid 30 through 315 or (resid 316 through 317 and (name N or n \ ame CA or name C or name O or name CB )) or resid 318 through 356 or (resid 357 \ and (name N or name CA or name C or name O or name CB )) or resid 358 through 39 \ 7 or (resid 398 and (name N or name CA or name C or name O or name CB )) or resi \ d 399 through 410 or (resid 416 through 422 and (name N or name CA or name C or \ name O or name CB )) or resid 423 or (resid 424 through 429 and (name N or name \ CA or name C or name O or name CB )) or resid 430 through 447 or (resid 448 thro \ ugh 449 and (name N or name CA or name C or name O or name CB )) or resid 450 or \ (resid 451 through 452 and (name N or name CA or name C or name O or name CB )) \ or resid 453 through 465 or (resid 466 through 467 and (name N or name CA or na \ me C or name O or name CB )) or resid 468 through 489 or (resid 490 and (name N \ or name CA or name C or name O or name CB )) or resid 491 through 500 or (resid \ 501 through 509 and (name N or name CA or name C or name O or name CB )) or resi \ d 600 through 601)) selection = (chain 'B' and ((resid 28 through 29 and (name N or name CA or name C or name O \ or name CB )) or resid 30 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 80 or (resid 81 and (name N or na \ me CA or name C or name O or name CB )) or resid 82 through 152 or (resid 153 th \ rough 154 and (name N or name CA or name C or name O or name CB )) or resid 155 \ through 182 or (resid 183 and (name N or name CA or name C or name O or name CB \ )) or resid 184 through 329 or (resid 330 and (name N or name CA or name C or na \ me O or name CB )) or resid 331 through 334 or (resid 335 and (name N or name CA \ or name C or name O or name CB )) or resid 336 through 360 or (resid 361 and (n \ ame N or name CA or name C or name O or name CB )) or resid 362 or (resid 363 an \ d (name N or name CA or name C or name O or name CB )) or resid 364 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 399 or (resid 400 through 401 and (name N or name CA or \ name C or name O or name CB )) or resid 402 through 404 or (resid 405 through 42 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 423 through \ 455 or (resid 456 and (name N or name CA or name C or name O or name CB )) or re \ sid 457 through 461 or (resid 462 and (name N or name CA or name C or name O or \ name CB )) or resid 463 through 479 or (resid 480 and (name N or name CA or name \ C or name O or name CB )) or resid 481 through 486 or (resid 487 through 488 an \ d (name N or name CA or name C or name O or name CB )) or resid 489 or (resid 49 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 491 through \ 492 or (resid 493 and (name N or name CA or name C or name O or name CB )) or re \ sid 494 through 509 or resid 600 through 601)) selection = (chain 'C' and (resid 28 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 through 80 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 152 or (resid 153 thr \ ough 154 and (name N or name CA or name C or name O or name CB )) or resid 155 t \ hrough 315 or (resid 316 through 317 and (name N or name CA or name C or name O \ or name CB )) or resid 318 through 329 or (resid 330 and (name N or name CA or n \ ame C or name O or name CB )) or resid 331 through 334 or (resid 335 and (name N \ or name CA or name C or name O or name CB )) or resid 336 through 356 or (resid \ 357 and (name N or name CA or name C or name O or name CB )) or resid 358 throu \ gh 360 or (resid 361 and (name N or name CA or name C or name O or name CB )) or \ resid 362 or (resid 363 and (name N or name CA or name C or name O or name CB ) \ ) or resid 364 through 382 or (resid 383 through 384 and (name N or name CA or n \ ame C or name O or name CB )) or resid 385 through 397 or (resid 398 and (name N \ or name CA or name C or name O or name CB )) or resid 399 or (resid 400 through \ 401 and (name N or name CA or name C or name O or name CB )) or resid 402 throu \ gh 404 or (resid 405 through 407 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 410 and (name N or name CA or name C or name O or name CB )) \ or (resid 416 through 422 and (name N or name CA or name C or name O or name CB \ )) or (resid 423 through 429 and (name N or name CA or name C or name O or name \ CB )) or resid 430 through 447 or (resid 448 through 449 and (name N or name CA \ or name C or name O or name CB )) or resid 450 or (resid 451 through 452 and (n \ ame N or name CA or name C or name O or name CB )) or resid 453 through 455 or ( \ resid 456 and (name N or name CA or name C or name O or name CB )) or resid 457 \ through 461 or (resid 462 and (name N or name CA or name C or name O or name CB \ )) or resid 463 through 465 or (resid 466 through 467 and (name N or name CA or \ name C or name O or name CB )) or resid 468 through 479 or (resid 480 and (name \ N or name CA or name C or name O or name CB )) or resid 481 through 487 or (resi \ d 488 and (name N or name CA or name C or name O or name CB )) or resid 489 thro \ ugh 499 or (resid 500 through 509 and (name N or name CA or name C or name O or \ name CB )) or resid 600 through 601)) } ncs_group { reference = (chain 'D' 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 111 or (resid 112 and (name N or na \ me CA or name C or name O or name CB )) or resid 113 through 400 or (resid 401 a \ nd (name N or name CA or name C or name O or name CB )) or resid 402 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 'E' and (resid 8 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 104 or (resid 105 and \ (name N or name CA or name C or name O or name CB )) or resid 106 through 209 or \ (resid 210 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 1 through 314 or (resid 315 and (name N or name CA or name C or name O or name C \ B )) or resid 316 through 318 or (resid 319 and (name N or name CA or name C or \ name O or name CB )) or resid 320 through 365 or (resid 366 and (name N or name \ CA or name C or name O or name CB )) or resid 367 through 381 or (resid 382 thro \ ugh 391 and (name N or name CA or name C or name O or name CB )) or (resid 392 t \ hrough 398 and (name N or name CA or name C or name O or name CB )) or resid 399 \ through 408 or (resid 409 and (name N or name CA or name C or name O or name CB \ )) or resid 410 through 471 or (resid 472 and (name N or name CA or name C or n \ ame O or name CB )) or resid 473 through 475)) selection = (chain 'F' and (resid 8 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 39 or (resid 40 and (name N or name \ CA or name C or name O or name CB )) or resid 41 through 42 or (resid 43 and (n \ ame N or name CA or name C or name O or name CB )) or resid 44 through 111 or (r \ esid 112 and (name N or name CA or name C or name O or name CB )) or resid 113 t \ hrough 211 or (resid 212 and (name N or name CA or name C or name O or name CB ) \ ) or resid 213 through 314 or (resid 315 and (name N or name CA or name C or nam \ e O or name CB )) or resid 316 through 318 or (resid 319 and (name N or name CA \ or name C or name O or name CB )) or resid 320 through 365 or (resid 366 and (na \ me N or name CA or name C or name O or name CB )) or resid 367 through 372 or (r \ esid 373 and (name N or name CA or name C or name O or name CB )) or resid 374 t \ hrough 375 or (resid 376 and (name N or name CA or name C or name O or name CB ) \ ) or resid 377 through 381 or (resid 382 through 391 and (name N or name CA or n \ ame C or name O or name CB )) or resid 392 or (resid 393 through 398 and (name N \ or name CA or name C or name O or name CB )) or resid 399 through 400 or (resid \ 401 and (name N or name CA or name C or name O or name CB )) or resid 402 throu \ gh 408 or (resid 409 and (name N or name CA or name C or name O or name CB )) or \ resid 410 through 434 or (resid 435 and (name N or name CA or name C or name O \ or name CB )) or resid 436 through 463 or (resid 464 and (name N or name CA or n \ ame C or name O or name CB )) or resid 465 through 471 or (resid 472 and (name N \ or name CA or name C or name O or name CB )) or resid 473 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.200 Check model and map are aligned: 0.430 Set scattering table: 0.230 Process input model: 63.060 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.002 0.061 23016 Z= 0.167 Angle : 0.587 6.635 31290 Z= 0.326 Chirality : 0.045 0.296 3744 Planarity : 0.004 0.054 4073 Dihedral : 12.530 89.629 8312 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.36 (0.15), residues: 3080 helix: 0.61 (0.14), residues: 1281 sheet: -0.08 (0.22), residues: 509 loop : 0.20 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 258 HIS 0.005 0.001 HIS A 478 PHE 0.012 0.001 PHE C 405 TYR 0.019 0.001 TYR B 399 ARG 0.014 0.001 ARG E 406 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 2.418 Fit side-chains REVERT: A 175 THR cc_start: 0.8821 (p) cc_final: 0.8476 (p) REVERT: A 271 ASP cc_start: 0.8255 (t0) cc_final: 0.7823 (t0) REVERT: A 454 HIS cc_start: 0.6536 (m90) cc_final: 0.6320 (m170) REVERT: B 64 MET cc_start: 0.8267 (ttt) cc_final: 0.7904 (ttm) REVERT: C 271 ASP cc_start: 0.7989 (t0) cc_final: 0.7526 (t0) REVERT: C 335 ASP cc_start: 0.8222 (t0) cc_final: 0.7963 (t0) REVERT: C 357 GLU cc_start: 0.7599 (mp0) cc_final: 0.7396 (mp0) REVERT: D 64 MET cc_start: 0.8602 (mmt) cc_final: 0.8370 (mmp) REVERT: D 127 GLN cc_start: 0.8393 (mm-40) cc_final: 0.7975 (mm-40) REVERT: E 64 MET cc_start: 0.9145 (mmt) cc_final: 0.8876 (mmt) REVERT: E 142 ASP cc_start: 0.6708 (m-30) cc_final: 0.6450 (m-30) REVERT: E 352 ASP cc_start: 0.8249 (m-30) cc_final: 0.8016 (m-30) REVERT: E 368 TYR cc_start: 0.8875 (t80) cc_final: 0.8580 (t80) REVERT: E 449 TYR cc_start: 0.8685 (m-80) cc_final: 0.8424 (m-80) REVERT: F 123 SER cc_start: 0.8842 (p) cc_final: 0.8583 (t) REVERT: F 393 MET cc_start: 0.8024 (mmm) cc_final: 0.7757 (mmm) REVERT: G 30 ARG cc_start: 0.5459 (mtt-85) cc_final: 0.5080 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.3972 time to fit residues: 247.1970 Evaluate side-chains 221 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 2.434 ------------------------------------------------------------------------------- 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: 8.9990 chunk 128 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 156 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 239 optimal weight: 0.0870 chunk 92 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 277 optimal weight: 4.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN A 304 HIS A 454 HIS B 192 ASN B 224 GLN D 263 GLN D 379 GLN ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 23016 Z= 0.350 Angle : 0.597 8.612 31290 Z= 0.310 Chirality : 0.047 0.166 3744 Planarity : 0.004 0.040 4073 Dihedral : 6.766 87.898 3417 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.25 % Allowed : 7.20 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.42 (0.15), residues: 3080 helix: 0.78 (0.15), residues: 1269 sheet: -0.27 (0.22), residues: 527 loop : 0.20 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 191 HIS 0.006 0.001 HIS B 478 PHE 0.020 0.002 PHE E 457 TYR 0.029 0.002 TYR B 399 ARG 0.006 0.001 ARG C 422 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 243 time to evaluate : 2.804 Fit side-chains revert: symmetry clash REVERT: A 271 ASP cc_start: 0.8359 (t0) cc_final: 0.7903 (t0) REVERT: B 64 MET cc_start: 0.8337 (ttt) cc_final: 0.8099 (ttm) REVERT: B 224 GLN cc_start: 0.7912 (mt0) cc_final: 0.7704 (tt0) REVERT: C 271 ASP cc_start: 0.8237 (t0) cc_final: 0.7958 (t0) REVERT: C 422 ARG cc_start: 0.8019 (tpp80) cc_final: 0.7773 (tpp80) REVERT: D 64 MET cc_start: 0.8757 (mmt) cc_final: 0.8501 (mmp) REVERT: D 256 ASP cc_start: 0.7260 (t0) cc_final: 0.6938 (t0) REVERT: D 334 VAL cc_start: 0.9122 (t) cc_final: 0.8894 (p) REVERT: D 401 LYS cc_start: 0.6791 (pttt) cc_final: 0.6056 (mttp) REVERT: E 375 GLN cc_start: 0.8473 (mt0) cc_final: 0.8257 (mt0) REVERT: E 449 TYR cc_start: 0.8837 (m-80) cc_final: 0.8502 (m-80) REVERT: F 393 MET cc_start: 0.8110 (mmm) cc_final: 0.7822 (mmm) REVERT: G 30 ARG cc_start: 0.5749 (mtt-85) cc_final: 0.4979 (tpp-160) outliers start: 28 outliers final: 19 residues processed: 259 average time/residue: 0.3655 time to fit residues: 145.0169 Evaluate side-chains 217 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 198 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 272 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 278 optimal weight: 0.4980 chunk 300 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 276 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 chunk 223 optimal weight: 5.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 ASN E 385 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 23016 Z= 0.460 Angle : 0.614 8.871 31290 Z= 0.318 Chirality : 0.048 0.169 3744 Planarity : 0.004 0.043 4073 Dihedral : 6.866 88.663 3417 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.06 % Allowed : 8.28 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.16 (0.15), residues: 3080 helix: 0.74 (0.15), residues: 1243 sheet: -0.40 (0.22), residues: 528 loop : -0.13 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 191 HIS 0.007 0.002 HIS B 478 PHE 0.020 0.002 PHE E 457 TYR 0.032 0.002 TYR B 399 ARG 0.006 0.001 ARG D 337 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 215 time to evaluate : 2.752 Fit side-chains revert: symmetry clash REVERT: A 271 ASP cc_start: 0.8444 (t0) cc_final: 0.7987 (t0) REVERT: A 355 GLU cc_start: 0.7249 (tp30) cc_final: 0.6959 (tt0) REVERT: A 501 SER cc_start: 0.8141 (t) cc_final: 0.7084 (p) REVERT: B 224 GLN cc_start: 0.7827 (mt0) cc_final: 0.7617 (tt0) REVERT: B 272 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8141 (p0) REVERT: C 271 ASP cc_start: 0.8364 (t0) cc_final: 0.8050 (t0) REVERT: C 422 ARG cc_start: 0.7959 (tpp80) cc_final: 0.7607 (tpp80) REVERT: D 64 MET cc_start: 0.8729 (mmt) cc_final: 0.8448 (mmp) REVERT: D 256 ASP cc_start: 0.7308 (t0) cc_final: 0.6995 (t70) REVERT: D 401 LYS cc_start: 0.6850 (pttt) cc_final: 0.6129 (mttp) REVERT: E 375 GLN cc_start: 0.8528 (mt0) cc_final: 0.8315 (mt0) REVERT: E 449 TYR cc_start: 0.8935 (m-80) cc_final: 0.8587 (m-80) REVERT: F 311 TYR cc_start: 0.8796 (t80) cc_final: 0.8584 (t80) REVERT: F 393 MET cc_start: 0.8179 (mmm) cc_final: 0.7927 (mmm) REVERT: G 30 ARG cc_start: 0.6014 (mtt-85) cc_final: 0.5086 (tpp-160) outliers start: 46 outliers final: 31 residues processed: 249 average time/residue: 0.3574 time to fit residues: 138.4561 Evaluate side-chains 230 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 198 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 30 THR 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 B residue 483 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 204 THR Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 272 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 186 optimal weight: 0.3980 chunk 279 optimal weight: 0.9990 chunk 295 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 418 GLN E 223 ASN F 172 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23016 Z= 0.232 Angle : 0.507 7.853 31290 Z= 0.263 Chirality : 0.044 0.173 3744 Planarity : 0.004 0.040 4073 Dihedral : 6.477 89.871 3417 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.79 % Allowed : 9.89 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.41 (0.15), residues: 3080 helix: 0.99 (0.15), residues: 1265 sheet: -0.21 (0.23), residues: 510 loop : -0.09 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 191 HIS 0.004 0.001 HIS B 478 PHE 0.014 0.001 PHE A 359 TYR 0.022 0.001 TYR B 399 ARG 0.003 0.000 ARG F 295 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 217 time to evaluate : 2.448 Fit side-chains revert: symmetry clash REVERT: A 355 GLU cc_start: 0.7209 (tp30) cc_final: 0.6908 (tt0) REVERT: B 355 GLU cc_start: 0.8004 (tt0) cc_final: 0.7763 (mt-10) REVERT: C 271 ASP cc_start: 0.8271 (t0) cc_final: 0.7900 (t0) REVERT: D 64 MET cc_start: 0.8702 (mmt) cc_final: 0.8432 (mmp) REVERT: D 256 ASP cc_start: 0.7219 (t0) cc_final: 0.6901 (t70) REVERT: D 401 LYS cc_start: 0.6956 (pttt) cc_final: 0.6225 (mttp) REVERT: E 375 GLN cc_start: 0.8506 (mt0) cc_final: 0.8270 (mt0) REVERT: E 449 TYR cc_start: 0.8902 (m-80) cc_final: 0.8663 (m-80) REVERT: F 311 TYR cc_start: 0.8775 (t80) cc_final: 0.8562 (t80) REVERT: F 393 MET cc_start: 0.8059 (mmm) cc_final: 0.7760 (mmm) REVERT: G 30 ARG cc_start: 0.5888 (mtt-85) cc_final: 0.5101 (tpp-160) outliers start: 40 outliers final: 27 residues processed: 243 average time/residue: 0.3336 time to fit residues: 127.2998 Evaluate side-chains 223 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 196 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 272 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 220 optimal weight: 0.0050 chunk 122 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 204 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 151 optimal weight: 0.3980 chunk 265 optimal weight: 0.6980 chunk 74 optimal weight: 0.0270 overall best weight: 0.3052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN C 304 HIS ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 23016 Z= 0.129 Angle : 0.459 8.686 31290 Z= 0.237 Chirality : 0.042 0.142 3744 Planarity : 0.003 0.039 4073 Dihedral : 5.913 81.902 3417 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.07 % Allowed : 10.51 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.81 (0.15), residues: 3080 helix: 1.33 (0.15), residues: 1273 sheet: 0.15 (0.24), residues: 485 loop : 0.03 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 191 HIS 0.002 0.000 HIS D 367 PHE 0.015 0.001 PHE A 359 TYR 0.022 0.001 TYR G 226 ARG 0.007 0.000 ARG C 422 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 231 time to evaluate : 2.777 Fit side-chains REVERT: A 355 GLU cc_start: 0.7125 (tp30) cc_final: 0.6921 (tt0) REVERT: B 355 GLU cc_start: 0.7983 (tt0) cc_final: 0.7770 (mt-10) REVERT: B 363 ILE cc_start: 0.8327 (mt) cc_final: 0.8066 (tt) REVERT: D 64 MET cc_start: 0.8692 (mmt) cc_final: 0.8421 (mmp) REVERT: D 256 ASP cc_start: 0.7271 (t0) cc_final: 0.6784 (t70) REVERT: D 375 GLN cc_start: 0.7775 (mt0) cc_final: 0.7551 (mt0) REVERT: D 401 LYS cc_start: 0.6963 (pttt) cc_final: 0.6269 (mttp) REVERT: E 375 GLN cc_start: 0.8445 (mt0) cc_final: 0.8068 (mt0) REVERT: E 449 TYR cc_start: 0.8824 (m-80) cc_final: 0.8543 (m-80) REVERT: F 393 MET cc_start: 0.8025 (mmm) cc_final: 0.7768 (mmm) REVERT: G 30 ARG cc_start: 0.5871 (mtt-85) cc_final: 0.4950 (tpp-160) REVERT: G 226 TYR cc_start: 0.6949 (t80) cc_final: 0.6688 (t80) outliers start: 24 outliers final: 17 residues processed: 243 average time/residue: 0.3485 time to fit residues: 131.8472 Evaluate side-chains 216 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 214 LEU Chi-restraints excluded: chain G residue 230 ILE 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: 3.9990 chunk 266 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 296 optimal weight: 0.9990 chunk 245 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 0.0060 chunk 155 optimal weight: 1.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23016 Z= 0.270 Angle : 0.509 8.209 31290 Z= 0.261 Chirality : 0.044 0.162 3744 Planarity : 0.004 0.055 4073 Dihedral : 6.055 85.138 3417 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.97 % Allowed : 10.78 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.71 (0.15), residues: 3080 helix: 1.29 (0.15), residues: 1263 sheet: -0.15 (0.23), residues: 543 loop : 0.07 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 191 HIS 0.005 0.001 HIS B 478 PHE 0.017 0.001 PHE A 359 TYR 0.023 0.001 TYR A 399 ARG 0.007 0.000 ARG C 422 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 197 time to evaluate : 2.749 Fit side-chains REVERT: B 272 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.8014 (p0) REVERT: B 355 GLU cc_start: 0.7938 (tt0) cc_final: 0.7722 (mt-10) REVERT: D 64 MET cc_start: 0.8729 (mmt) cc_final: 0.8419 (mmp) REVERT: D 256 ASP cc_start: 0.7219 (t0) cc_final: 0.6808 (t70) REVERT: D 401 LYS cc_start: 0.6884 (pttt) cc_final: 0.6207 (mttp) REVERT: E 375 GLN cc_start: 0.8489 (mt0) cc_final: 0.8105 (mt0) REVERT: F 393 MET cc_start: 0.8045 (mmm) cc_final: 0.7839 (mmm) REVERT: G 30 ARG cc_start: 0.6021 (mtt-85) cc_final: 0.4990 (tpp-160) outliers start: 44 outliers final: 33 residues processed: 223 average time/residue: 0.3568 time to fit residues: 124.8221 Evaluate side-chains 221 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 59 SER 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 B residue 336 VAL Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 369 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 422 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 272 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 168 optimal weight: 7.9990 chunk 216 optimal weight: 0.0060 chunk 167 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 294 optimal weight: 20.0000 chunk 184 optimal weight: 0.0020 chunk 179 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 418 GLN E 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23016 Z= 0.226 Angle : 0.491 8.737 31290 Z= 0.252 Chirality : 0.043 0.175 3744 Planarity : 0.003 0.039 4073 Dihedral : 6.021 84.912 3417 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.97 % Allowed : 11.01 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.70 (0.15), residues: 3080 helix: 1.29 (0.15), residues: 1272 sheet: -0.13 (0.23), residues: 540 loop : 0.03 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 191 HIS 0.004 0.001 HIS B 478 PHE 0.009 0.001 PHE B 470 TYR 0.019 0.001 TYR B 399 ARG 0.007 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 193 time to evaluate : 2.763 Fit side-chains revert: symmetry clash REVERT: B 272 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7940 (p0) REVERT: B 355 GLU cc_start: 0.7918 (tt0) cc_final: 0.7708 (mt-10) REVERT: D 64 MET cc_start: 0.8725 (mmt) cc_final: 0.8419 (mmp) REVERT: D 222 MET cc_start: 0.7370 (mtp) cc_final: 0.7035 (mtt) REVERT: D 256 ASP cc_start: 0.7232 (t0) cc_final: 0.6808 (t70) REVERT: D 401 LYS cc_start: 0.6889 (pttt) cc_final: 0.6207 (mttp) REVERT: E 375 GLN cc_start: 0.8507 (mt0) cc_final: 0.8133 (mt0) REVERT: F 393 MET cc_start: 0.8036 (mmm) cc_final: 0.7825 (mmm) REVERT: G 30 ARG cc_start: 0.5842 (mtt-85) cc_final: 0.4809 (tpp-160) outliers start: 44 outliers final: 34 residues processed: 219 average time/residue: 0.3448 time to fit residues: 118.2011 Evaluate side-chains 218 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 59 SER 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 B residue 336 VAL Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 412 ARG Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 272 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 187 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 231 optimal weight: 4.9990 chunk 268 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 178 HIS E 223 ASN F 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23016 Z= 0.170 Angle : 0.469 9.084 31290 Z= 0.241 Chirality : 0.042 0.187 3744 Planarity : 0.003 0.038 4073 Dihedral : 5.892 84.404 3417 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.92 % Allowed : 11.23 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.81 (0.15), residues: 3080 helix: 1.37 (0.15), residues: 1278 sheet: -0.02 (0.23), residues: 531 loop : 0.07 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 191 HIS 0.003 0.001 HIS B 478 PHE 0.008 0.001 PHE F 326 TYR 0.036 0.001 TYR A 399 ARG 0.007 0.000 ARG A 364 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 197 time to evaluate : 2.525 Fit side-chains revert: symmetry clash REVERT: A 447 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7158 (tp) REVERT: B 355 GLU cc_start: 0.7918 (tt0) cc_final: 0.7704 (mt-10) REVERT: D 64 MET cc_start: 0.8717 (mmt) cc_final: 0.8421 (mmp) REVERT: D 222 MET cc_start: 0.7347 (mtp) cc_final: 0.7037 (mtt) REVERT: D 256 ASP cc_start: 0.7204 (t0) cc_final: 0.6773 (t70) REVERT: D 401 LYS cc_start: 0.6970 (pttt) cc_final: 0.6310 (mttp) REVERT: E 375 GLN cc_start: 0.8486 (mt0) cc_final: 0.8107 (mt0) REVERT: F 393 MET cc_start: 0.7948 (mmm) cc_final: 0.7738 (mmm) REVERT: G 30 ARG cc_start: 0.5819 (mtt-85) cc_final: 0.4792 (tpp-160) outliers start: 43 outliers final: 36 residues processed: 223 average time/residue: 0.3497 time to fit residues: 122.5836 Evaluate side-chains 228 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 191 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 412 ARG Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain G residue 230 ILE 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: 9.9990 chunk 257 optimal weight: 0.6980 chunk 274 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 248 optimal weight: 0.4980 chunk 259 optimal weight: 3.9990 chunk 273 optimal weight: 4.9990 chunk 180 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: E 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 23016 Z= 0.381 Angle : 0.555 8.715 31290 Z= 0.286 Chirality : 0.046 0.175 3744 Planarity : 0.004 0.039 4073 Dihedral : 6.201 88.608 3417 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.01 % Allowed : 11.28 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.54 (0.15), residues: 3080 helix: 1.18 (0.15), residues: 1258 sheet: -0.23 (0.23), residues: 539 loop : -0.06 (0.17), residues: 1283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 191 HIS 0.006 0.001 HIS B 478 PHE 0.019 0.002 PHE A 359 TYR 0.030 0.002 TYR B 399 ARG 0.007 0.000 ARG C 422 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 188 time to evaluate : 2.674 Fit side-chains revert: symmetry clash REVERT: A 447 ILE cc_start: 0.7487 (OUTLIER) cc_final: 0.7210 (tp) REVERT: B 355 GLU cc_start: 0.7910 (tt0) cc_final: 0.7709 (mt-10) REVERT: C 422 ARG cc_start: 0.8746 (tpp80) cc_final: 0.8158 (tpp80) REVERT: D 64 MET cc_start: 0.8761 (mmt) cc_final: 0.8446 (mmp) REVERT: D 222 MET cc_start: 0.7476 (mtp) cc_final: 0.7145 (mtt) REVERT: D 401 LYS cc_start: 0.6991 (pttt) cc_final: 0.6308 (mttp) REVERT: E 375 GLN cc_start: 0.8489 (mt0) cc_final: 0.8125 (mt0) REVERT: F 393 MET cc_start: 0.8018 (mmm) cc_final: 0.7767 (mmm) REVERT: G 30 ARG cc_start: 0.5910 (mtt-85) cc_final: 0.4873 (tpp-160) outliers start: 45 outliers final: 40 residues processed: 216 average time/residue: 0.3400 time to fit residues: 115.4766 Evaluate side-chains 219 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 178 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 412 ARG Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain G residue 272 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 50.0000 chunk 177 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 202 optimal weight: 0.2980 chunk 304 optimal weight: 10.0000 chunk 280 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23016 Z= 0.177 Angle : 0.479 9.387 31290 Z= 0.247 Chirality : 0.043 0.189 3744 Planarity : 0.003 0.039 4073 Dihedral : 6.022 89.758 3417 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.88 % Allowed : 11.23 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.74 (0.15), residues: 3080 helix: 1.35 (0.15), residues: 1271 sheet: -0.07 (0.23), residues: 527 loop : -0.01 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 258 HIS 0.003 0.001 HIS B 478 PHE 0.015 0.001 PHE E 424 TYR 0.020 0.001 TYR A 399 ARG 0.006 0.000 ARG A 364 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6160 Ramachandran restraints generated. 3080 Oldfield, 0 Emsley, 3080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 196 time to evaluate : 2.607 Fit side-chains revert: symmetry clash REVERT: A 447 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7154 (tp) REVERT: B 355 GLU cc_start: 0.7904 (tt0) cc_final: 0.7703 (mt-10) REVERT: C 398 GLN cc_start: 0.8268 (mm-40) cc_final: 0.8018 (mt0) REVERT: D 64 MET cc_start: 0.8691 (mmt) cc_final: 0.8393 (mmp) REVERT: D 222 MET cc_start: 0.7387 (mtp) cc_final: 0.7131 (mtt) REVERT: D 401 LYS cc_start: 0.6992 (pttt) cc_final: 0.6311 (mttp) REVERT: E 375 GLN cc_start: 0.8466 (mt0) cc_final: 0.8082 (mt0) REVERT: F 281 TYR cc_start: 0.9338 (m-80) cc_final: 0.8769 (m-80) REVERT: F 393 MET cc_start: 0.7968 (mmm) cc_final: 0.7726 (mmm) REVERT: G 30 ARG cc_start: 0.5821 (mtt-85) cc_final: 0.4788 (tpp-160) outliers start: 42 outliers final: 39 residues processed: 221 average time/residue: 0.3459 time to fit residues: 119.4624 Evaluate side-chains 228 residues out of total 2515 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 188 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 203 CYS Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 447 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 412 ARG Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 136 THR Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 256 ASP Chi-restraints excluded: chain E residue 432 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 229 GLU Chi-restraints excluded: chain G residue 230 ILE 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: 0.9980 chunk 74 optimal weight: 0.6980 chunk 223 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.131991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105972 restraints weight = 29966.186| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.70 r_work: 0.3087 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23016 Z= 0.266 Angle : 0.504 9.047 31290 Z= 0.260 Chirality : 0.044 0.180 3744 Planarity : 0.004 0.039 4073 Dihedral : 6.049 89.692 3417 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.83 % Allowed : 11.50 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.70 (0.15), residues: 3080 helix: 1.31 (0.15), residues: 1271 sheet: -0.12 (0.23), residues: 538 loop : -0.00 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 191 HIS 0.004 0.001 HIS B 478 PHE 0.019 0.001 PHE A 359 TYR 0.027 0.001 TYR A 473 ARG 0.005 0.000 ARG A 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4429.41 seconds wall clock time: 80 minutes 41.56 seconds (4841.56 seconds total)