Starting phenix.real_space_refine on Fri Jan 24 09:19:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wm3_37639/01_2025/8wm3_37639_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wm3_37639/01_2025/8wm3_37639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wm3_37639/01_2025/8wm3_37639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wm3_37639/01_2025/8wm3_37639.map" model { file = "/net/cci-nas-00/data/ceres_data/8wm3_37639/01_2025/8wm3_37639_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wm3_37639/01_2025/8wm3_37639_neut.cif" } resolution = 3.34 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= 0.009 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 134 5.16 5 C 14016 2.51 5 N 3458 2.21 5 O 4008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 21616 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 4492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4492 Classifications: {'peptide': 572} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 551} Chain: "B" Number of atoms: 6095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6095 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Chain: "C" Number of atoms: 4492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4492 Classifications: {'peptide': 572} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 551} Chain: "D" Number of atoms: 6095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6095 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'TGI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'NAG': 1, 'TGI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.83, per 1000 atoms: 0.59 Number of scatterers: 21616 At special positions: 0 Unit cell: (132.495, 102.93, 180.675, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 134 16.00 O 4008 8.00 N 3458 7.00 C 14016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.06 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A 601 " - " ASN A 131 " " NAG B 901 " - " ASN B 322 " " NAG C 601 " - " ASN C 131 " " NAG D 901 " - " ASN D 322 " " NAG E 1 " - " ASN A 357 " " NAG F 1 " - " ASN B 546 " " NAG G 1 " - " ASN B 432 " " NAG H 1 " - " ASN B 90 " " NAG I 1 " - " ASN B 690 " " NAG K 1 " - " ASN B 103 " " NAG L 1 " - " ASN D 546 " " NAG M 1 " - " ASN D 432 " " NAG N 1 " - " ASN D 90 " " NAG O 1 " - " ASN D 690 " " NAG Q 1 " - " ASN D 103 " " NAG R 1 " - " ASN C 357 " Time building additional restraints: 6.35 Conformation dependent library (CDL) restraints added in 2.7 seconds 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4960 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 10 sheets defined 70.5% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 3.542A pdb=" N PHE A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 24 through 29 removed outlier: 3.935A pdb=" N VAL A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 40 through 53 removed outlier: 3.664A pdb=" N VAL A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Proline residue: A 46 - end of helix removed outlier: 3.643A pdb=" N VAL A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 70 removed outlier: 3.548A pdb=" N LEU A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 82 through 85 Processing helix chain 'A' and resid 86 through 116 removed outlier: 3.798A pdb=" N TYR A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE A 105 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 142 removed outlier: 3.584A pdb=" N GLU A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 151 Processing helix chain 'A' and resid 168 through 188 Processing helix chain 'A' and resid 195 through 216 Proline residue: A 203 - end of helix removed outlier: 3.771A pdb=" N ILE A 209 " --> pdb=" O CYS A 205 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 3.979A pdb=" N GLY A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.176A pdb=" N ASN A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 253 Processing helix chain 'A' and resid 257 through 266 removed outlier: 3.809A pdb=" N ALA A 261 " --> pdb=" O GLY A 257 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 322 removed outlier: 3.647A pdb=" N ILE A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 344 Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.697A pdb=" N TYR A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 379 " --> pdb=" O PHE A 375 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 420 removed outlier: 3.883A pdb=" N TRP A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Proline residue: A 417 - end of helix removed outlier: 4.096A pdb=" N ASP A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 426 Processing helix chain 'A' and resid 429 through 445 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 452 through 462 removed outlier: 3.931A pdb=" N TRP A 456 " --> pdb=" O ALA A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 482 removed outlier: 4.130A pdb=" N LEU A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 511 removed outlier: 3.912A pdb=" N TRP A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 532 removed outlier: 3.952A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL A 518 " --> pdb=" O PRO A 514 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 520 " --> pdb=" O LEU A 516 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE A 521 " --> pdb=" O ILE A 517 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 568 removed outlier: 3.607A pdb=" N SER A 566 " --> pdb=" O LEU A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 583 removed outlier: 4.221A pdb=" N VAL A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN A 580 " --> pdb=" O GLY A 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 53 removed outlier: 4.279A pdb=" N HIS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 81 Processing helix chain 'B' and resid 90 through 102 removed outlier: 4.167A pdb=" N GLN B 96 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.645A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 130 Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 157 through 194 removed outlier: 3.592A pdb=" N ARG B 169 " --> pdb=" O TRP B 165 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLN B 175 " --> pdb=" O GLU B 171 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 3.937A pdb=" N VAL B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 220 through 248 removed outlier: 3.945A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU B 232 " --> pdb=" O HIS B 228 " (cutoff:3.500A) Proline residue: B 235 - end of helix Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 282 removed outlier: 4.265A pdb=" N SER B 280 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 305 through 319 removed outlier: 3.586A pdb=" N LYS B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.641A pdb=" N TYR B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 400 through 414 removed outlier: 3.599A pdb=" N VAL B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 405 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 412 " --> pdb=" O MET B 408 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 413 " --> pdb=" O SER B 409 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.517A pdb=" N LEU B 418 " --> pdb=" O THR B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 465 removed outlier: 3.637A pdb=" N GLU B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR B 449 " --> pdb=" O THR B 445 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 450 " --> pdb=" O ILE B 446 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.894A pdb=" N LYS B 476 " --> pdb=" O GLN B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 503 Processing helix chain 'B' and resid 505 through 509 removed outlier: 3.598A pdb=" N ASP B 509 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 531 removed outlier: 3.524A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN B 531 " --> pdb=" O GLU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 547 through 559 removed outlier: 3.633A pdb=" N GLY B 551 " --> pdb=" O SER B 547 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 574 Processing helix chain 'B' and resid 581 through 599 Proline residue: B 590 - end of helix Processing helix chain 'B' and resid 623 through 628 removed outlier: 3.722A pdb=" N ALA B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 658 Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 696 through 713 removed outlier: 3.535A pdb=" N VAL B 700 " --> pdb=" O PRO B 696 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N SER B 709 " --> pdb=" O ARG B 705 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ARG B 710 " --> pdb=" O MET B 706 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 740 through 768 removed outlier: 3.741A pdb=" N ILE B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 20 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 30 through 38 Processing helix chain 'C' and resid 40 through 54 removed outlier: 3.527A pdb=" N LEU C 44 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL C 45 " --> pdb=" O GLY C 41 " (cutoff:3.500A) Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 54 through 70 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 86 through 116 removed outlier: 3.968A pdb=" N TYR C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL C 104 " --> pdb=" O MET C 100 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE C 105 " --> pdb=" O TYR C 101 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN C 106 " --> pdb=" O TYR C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 142 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 168 through 188 removed outlier: 3.706A pdb=" N GLY C 188 " --> pdb=" O CYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 216 removed outlier: 4.302A pdb=" N PHE C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Proline residue: C 203 - end of helix removed outlier: 3.923A pdb=" N ILE C 209 " --> pdb=" O CYS C 205 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 229 removed outlier: 4.286A pdb=" N GLY C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.902A pdb=" N ASN C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 253 removed outlier: 3.517A pdb=" N ILE C 242 " --> pdb=" O PRO C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 266 removed outlier: 3.815A pdb=" N ALA C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 322 removed outlier: 3.725A pdb=" N ILE C 297 " --> pdb=" O VAL C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 344 Processing helix chain 'C' and resid 344 through 352 Processing helix chain 'C' and resid 353 through 355 No H-bonds generated for 'chain 'C' and resid 353 through 355' Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 372 through 383 removed outlier: 3.556A pdb=" N TYR C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C 379 " --> pdb=" O PHE C 375 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU C 380 " --> pdb=" O ILE C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 420 removed outlier: 3.895A pdb=" N TRP C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) Proline residue: C 417 - end of helix removed outlier: 3.664A pdb=" N ASP C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 426 Processing helix chain 'C' and resid 429 through 445 Processing helix chain 'C' and resid 446 through 449 Processing helix chain 'C' and resid 452 through 462 removed outlier: 3.950A pdb=" N TRP C 456 " --> pdb=" O ALA C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 482 removed outlier: 3.839A pdb=" N LEU C 471 " --> pdb=" O LEU C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 511 through 532 removed outlier: 4.570A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 520 " --> pdb=" O LEU C 516 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 521 " --> pdb=" O ILE C 517 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE C 523 " --> pdb=" O SER C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 568 removed outlier: 3.780A pdb=" N SER C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 583 removed outlier: 3.514A pdb=" N LEU C 572 " --> pdb=" O MET C 568 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN C 580 " --> pdb=" O GLY C 576 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C 583 " --> pdb=" O VAL C 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 53 removed outlier: 4.113A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 102 removed outlier: 4.236A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.804A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 193 removed outlier: 3.585A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 4.096A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 220 through 252 removed outlier: 3.793A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 4.197A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 282 removed outlier: 4.518A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.981A pdb=" N MET D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 319 removed outlier: 3.681A pdb=" N LYS D 309 " --> pdb=" O GLN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 330 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.647A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 400 through 414 removed outlier: 3.524A pdb=" N VAL D 404 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR D 414 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 465 removed outlier: 3.610A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR D 449 " --> pdb=" O THR D 445 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU D 450 " --> pdb=" O ILE D 446 " (cutoff:3.500A) Proline residue: D 451 - end of helix Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.927A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 503 Processing helix chain 'D' and resid 505 through 509 removed outlier: 3.688A pdb=" N ASP D 509 " --> pdb=" O VAL D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 530 removed outlier: 3.727A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.577A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 573 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'D' and resid 623 through 628 removed outlier: 3.581A pdb=" N ALA D 627 " --> pdb=" O SER D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 658 removed outlier: 3.544A pdb=" N MET D 640 " --> pdb=" O ASN D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 668 No H-bonds generated for 'chain 'D' and resid 666 through 668' Processing helix chain 'D' and resid 696 through 713 removed outlier: 3.648A pdb=" N VAL D 700 " --> pdb=" O PRO D 696 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N SER D 709 " --> pdb=" O ARG D 705 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ARG D 710 " --> pdb=" O MET D 706 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP D 713 " --> pdb=" O SER D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 716 No H-bonds generated for 'chain 'D' and resid 714 through 716' Processing helix chain 'D' and resid 740 through 767 removed outlier: 3.663A pdb=" N ILE D 744 " --> pdb=" O SER D 740 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 535 through 538 Processing sheet with id=AA2, first strand: chain 'B' and resid 262 through 263 removed outlier: 5.993A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 347 through 348 Processing sheet with id=AA4, first strand: chain 'B' and resid 670 through 673 removed outlier: 7.086A pdb=" N ASP B 693 " --> pdb=" O ALA B 687 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 670 through 673 removed outlier: 3.503A pdb=" N GLU B 723 " --> pdb=" O ARG B 621 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 535 through 538 Processing sheet with id=AA7, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.838A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 347 through 348 Processing sheet with id=AA9, first strand: chain 'D' and resid 670 through 673 removed outlier: 7.071A pdb=" N ASP D 693 " --> pdb=" O ALA D 687 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 670 through 673 removed outlier: 3.563A pdb=" N GLU D 723 " --> pdb=" O ARG D 621 " (cutoff:3.500A) 1213 hydrogen bonds defined for protein. 3534 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: 6.44 Time building geometry restraints manager: 7.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3444 1.31 - 1.44: 6376 1.44 - 1.57: 12148 1.57 - 1.70: 8 1.70 - 1.83: 216 Bond restraints: 22192 Sorted by residual: bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.536 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C5 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.413 1.532 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" C5 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.413 1.531 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" C5 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.413 1.531 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" C5 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.413 1.531 -0.118 2.00e-02 2.50e+03 3.46e+01 ... (remaining 22187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 29781 2.96 - 5.92: 328 5.92 - 8.88: 56 8.88 - 11.83: 11 11.83 - 14.79: 6 Bond angle restraints: 30182 Sorted by residual: angle pdb=" C MET A 508 " pdb=" N TRP A 509 " pdb=" CA TRP A 509 " ideal model delta sigma weight residual 122.65 114.23 8.42 1.60e+00 3.91e-01 2.77e+01 angle pdb=" C08 TGI C 602 " pdb=" C07 TGI C 602 " pdb=" C20 TGI C 602 " ideal model delta sigma weight residual 122.61 107.82 14.79 3.00e+00 1.11e-01 2.43e+01 angle pdb=" C08 TGI A 602 " pdb=" C07 TGI A 602 " pdb=" C20 TGI A 602 " ideal model delta sigma weight residual 122.61 107.85 14.76 3.00e+00 1.11e-01 2.42e+01 angle pdb=" N GLN B 305 " pdb=" CA GLN B 305 " pdb=" C GLN B 305 " ideal model delta sigma weight residual 114.62 109.07 5.55 1.14e+00 7.69e-01 2.37e+01 angle pdb=" N GLN D 305 " pdb=" CA GLN D 305 " pdb=" C GLN D 305 " ideal model delta sigma weight residual 114.62 109.10 5.52 1.14e+00 7.69e-01 2.34e+01 ... (remaining 30177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.04: 12314 25.04 - 50.07: 850 50.07 - 75.11: 136 75.11 - 100.15: 54 100.15 - 125.19: 46 Dihedral angle restraints: 13400 sinusoidal: 5668 harmonic: 7732 Sorted by residual: dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 141 " pdb=" CB CYS B 141 " ideal model delta sinusoidal sigma weight residual 93.00 38.08 54.92 1 1.00e+01 1.00e-02 4.08e+01 dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 45.40 47.60 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CB CYS D 530 " pdb=" SG CYS D 530 " pdb=" SG CYS D 542 " pdb=" CB CYS D 542 " ideal model delta sinusoidal sigma weight residual -86.00 -130.83 44.83 1 1.00e+01 1.00e-02 2.79e+01 ... (remaining 13397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.221: 3370 0.221 - 0.443: 12 0.443 - 0.664: 0 0.664 - 0.885: 1 0.885 - 1.106: 1 Chirality restraints: 3384 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-02 2.50e+03 3.57e+02 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-02 2.50e+03 3.30e+02 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.93e+01 ... (remaining 3381 not shown) Planarity restraints: 3786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " 0.353 2.00e-02 2.50e+03 3.03e-01 1.14e+03 pdb=" C7 NAG K 1 " -0.088 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " 0.153 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " -0.537 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " 0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG G 2 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " -0.532 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 2 " 0.345 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG L 2 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG L 2 " 0.155 2.00e-02 2.50e+03 pdb=" N2 NAG L 2 " -0.526 2.00e-02 2.50e+03 pdb=" O7 NAG L 2 " 0.110 2.00e-02 2.50e+03 ... (remaining 3783 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 869 2.72 - 3.26: 23487 3.26 - 3.81: 36405 3.81 - 4.35: 42075 4.35 - 4.90: 70303 Nonbonded interactions: 173139 Sorted by model distance: nonbonded pdb=" ND2 ASN C 461 " pdb=" OD1 ASP C 462 " model vdw 2.169 3.120 nonbonded pdb=" OG SER A 359 " pdb=" OG SER A 362 " model vdw 2.201 3.040 nonbonded pdb=" OG SER D 109 " pdb=" OD1 ASP D 111 " model vdw 2.209 3.040 nonbonded pdb=" NZ LYS D 419 " pdb=" O PHE D 428 " model vdw 2.214 3.120 nonbonded pdb=" OD1 ASN B 53 " pdb=" NE2 GLN B 340 " model vdw 2.218 3.120 ... (remaining 173134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' } 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: 1.010 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: 0.050 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 46.760 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 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 : 0.006 0.123 22192 Z= 0.407 Angle : 0.794 14.793 30182 Z= 0.392 Chirality : 0.052 1.106 3384 Planarity : 0.018 0.303 3770 Dihedral : 19.233 125.187 8410 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.86 % Rotamer: Outliers : 0.91 % Allowed : 17.51 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % 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: 0.99 (0.17), residues: 2634 helix: 1.64 (0.13), residues: 1580 sheet: -1.48 (0.73), residues: 40 loop : -0.81 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 509 HIS 0.009 0.001 HIS D 374 PHE 0.061 0.001 PHE C 96 TYR 0.013 0.001 TYR C 395 ARG 0.006 0.000 ARG D 678 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8146 (t0) REVERT: B 376 MET cc_start: 0.9442 (tpt) cc_final: 0.9027 (tpt) REVERT: D 249 MET cc_start: 0.9070 (mmm) cc_final: 0.8870 (mmt) REVERT: D 455 MET cc_start: 0.9193 (tmm) cc_final: 0.8730 (tmm) outliers start: 21 outliers final: 10 residues processed: 129 average time/residue: 0.3210 time to fit residues: 69.0366 Evaluate side-chains 118 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 30.0000 chunk 198 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 237 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 GLN C 118 GLN D 401 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.054315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.038102 restraints weight = 135829.089| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 4.77 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22192 Z= 0.287 Angle : 0.686 11.196 30182 Z= 0.326 Chirality : 0.045 0.540 3384 Planarity : 0.004 0.036 3770 Dihedral : 14.581 111.697 3521 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.35 % Allowed : 16.11 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.17), residues: 2634 helix: 1.92 (0.13), residues: 1628 sheet: -1.35 (0.78), residues: 40 loop : -0.80 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 509 HIS 0.008 0.001 HIS D 374 PHE 0.016 0.001 PHE D 523 TYR 0.025 0.001 TYR A 21 ARG 0.004 0.000 ARG D 678 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 113 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.9224 (OUTLIER) cc_final: 0.8936 (t) REVERT: A 402 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9111 (mp) REVERT: B 332 MET cc_start: 0.8038 (ptt) cc_final: 0.7780 (ptt) REVERT: B 376 MET cc_start: 0.9395 (tpt) cc_final: 0.8811 (tpt) REVERT: B 470 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.8901 (ttmm) REVERT: B 640 MET cc_start: 0.9420 (mmm) cc_final: 0.9124 (tpp) REVERT: C 91 SER cc_start: 0.9014 (OUTLIER) cc_final: 0.8761 (t) REVERT: C 463 TYR cc_start: 0.8843 (t80) cc_final: 0.8481 (t80) REVERT: D 408 MET cc_start: 0.8889 (tpp) cc_final: 0.8261 (tpp) REVERT: D 455 MET cc_start: 0.9057 (tmm) cc_final: 0.8476 (tmm) REVERT: D 723 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8461 (mp0) outliers start: 54 outliers final: 24 residues processed: 160 average time/residue: 0.3132 time to fit residues: 83.6481 Evaluate side-chains 138 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 503 TRP Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 723 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 123 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 250 optimal weight: 0.8980 chunk 137 optimal weight: 30.0000 chunk 92 optimal weight: 30.0000 chunk 83 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 110 optimal weight: 30.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 325 GLN C 266 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.054522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.038256 restraints weight = 134414.127| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 4.79 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22192 Z= 0.195 Angle : 0.625 11.455 30182 Z= 0.294 Chirality : 0.043 0.389 3384 Planarity : 0.003 0.035 3770 Dihedral : 13.132 109.106 3515 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.00 % Allowed : 16.86 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.17), residues: 2634 helix: 2.05 (0.13), residues: 1638 sheet: -1.19 (0.81), residues: 40 loop : -0.79 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 509 HIS 0.007 0.001 HIS D 374 PHE 0.023 0.001 PHE A 96 TYR 0.034 0.001 TYR A 21 ARG 0.003 0.000 ARG D 678 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 108 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 332 MET cc_start: 0.7739 (ptt) cc_final: 0.7442 (ptt) REVERT: B 376 MET cc_start: 0.9368 (tpt) cc_final: 0.8701 (tpt) REVERT: B 408 MET cc_start: 0.9693 (mmm) cc_final: 0.9324 (mmm) REVERT: B 470 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.8985 (ttmm) REVERT: B 640 MET cc_start: 0.9380 (mmm) cc_final: 0.9096 (tpp) REVERT: B 723 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: D 332 MET cc_start: 0.8859 (tpp) cc_final: 0.8591 (tpp) REVERT: D 408 MET cc_start: 0.8972 (tpp) cc_final: 0.8288 (tpp) REVERT: D 455 MET cc_start: 0.9054 (tmm) cc_final: 0.8547 (tmm) REVERT: D 723 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8439 (mp0) outliers start: 46 outliers final: 27 residues processed: 143 average time/residue: 0.2874 time to fit residues: 69.2882 Evaluate side-chains 137 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 503 TRP Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 723 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 179 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 145 optimal weight: 0.2980 chunk 154 optimal weight: 1.9990 chunk 205 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 135 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN C 167 GLN C 266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.053848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.037464 restraints weight = 136576.634| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 4.78 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22192 Z= 0.236 Angle : 0.629 10.629 30182 Z= 0.299 Chirality : 0.043 0.322 3384 Planarity : 0.003 0.038 3770 Dihedral : 11.799 104.792 3513 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.31 % Allowed : 17.16 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.17), residues: 2634 helix: 2.14 (0.13), residues: 1642 sheet: -1.13 (0.83), residues: 40 loop : -0.72 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 509 HIS 0.007 0.001 HIS D 374 PHE 0.027 0.001 PHE B 746 TYR 0.030 0.001 TYR A 21 ARG 0.005 0.000 ARG B 678 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 107 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.9214 (OUTLIER) cc_final: 0.8939 (t) REVERT: A 172 LEU cc_start: 0.8746 (pp) cc_final: 0.8533 (pp) REVERT: A 385 MET cc_start: 0.9338 (mmt) cc_final: 0.9101 (mmp) REVERT: B 332 MET cc_start: 0.7724 (ptt) cc_final: 0.7367 (ptt) REVERT: B 375 GLU cc_start: 0.9518 (OUTLIER) cc_final: 0.9257 (mm-30) REVERT: B 376 MET cc_start: 0.9425 (tpt) cc_final: 0.9040 (tpt) REVERT: B 470 LYS cc_start: 0.9356 (OUTLIER) cc_final: 0.9009 (ttmm) REVERT: B 640 MET cc_start: 0.9415 (mmm) cc_final: 0.9097 (tpp) REVERT: B 723 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8323 (mp0) REVERT: C 91 SER cc_start: 0.9026 (OUTLIER) cc_final: 0.8757 (t) REVERT: D 332 MET cc_start: 0.9047 (tpp) cc_final: 0.8713 (tpp) REVERT: D 376 MET cc_start: 0.9411 (tpt) cc_final: 0.9173 (tpt) REVERT: D 408 MET cc_start: 0.9078 (tpp) cc_final: 0.8402 (tpp) REVERT: D 455 MET cc_start: 0.9116 (tmm) cc_final: 0.8577 (tmm) outliers start: 53 outliers final: 36 residues processed: 151 average time/residue: 0.3020 time to fit residues: 76.3466 Evaluate side-chains 146 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 168 TRP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 503 TRP Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 362 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 81 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 chunk 127 optimal weight: 0.0170 chunk 47 optimal weight: 9.9990 chunk 201 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 overall best weight: 3.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.053741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.037374 restraints weight = 134842.640| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 4.75 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22192 Z= 0.210 Angle : 0.614 10.822 30182 Z= 0.291 Chirality : 0.043 0.302 3384 Planarity : 0.003 0.038 3770 Dihedral : 11.044 103.128 3513 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.35 % Allowed : 17.90 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.17), residues: 2634 helix: 2.18 (0.13), residues: 1644 sheet: -1.03 (0.84), residues: 40 loop : -0.67 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 509 HIS 0.010 0.001 HIS B 374 PHE 0.013 0.001 PHE A 96 TYR 0.022 0.001 TYR A 21 ARG 0.004 0.000 ARG B 678 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 110 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.9225 (OUTLIER) cc_final: 0.8964 (t) REVERT: A 402 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9139 (mp) REVERT: B 332 MET cc_start: 0.7762 (ptt) cc_final: 0.7341 (ptt) REVERT: B 360 MET cc_start: 0.8910 (ppp) cc_final: 0.8710 (ppp) REVERT: B 376 MET cc_start: 0.9381 (tpt) cc_final: 0.8674 (tpt) REVERT: B 408 MET cc_start: 0.9674 (mmm) cc_final: 0.9372 (mmm) REVERT: B 455 MET cc_start: 0.9094 (tmm) cc_final: 0.8485 (tmm) REVERT: B 640 MET cc_start: 0.9376 (mmm) cc_final: 0.9069 (tpp) REVERT: B 651 MET cc_start: 0.9312 (mmm) cc_final: 0.8939 (mmm) REVERT: B 723 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8221 (mp0) REVERT: C 91 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8770 (t) REVERT: C 189 THR cc_start: 0.7297 (OUTLIER) cc_final: 0.6917 (p) REVERT: C 527 ASP cc_start: 0.9532 (OUTLIER) cc_final: 0.9232 (m-30) REVERT: D 332 MET cc_start: 0.9216 (tpp) cc_final: 0.8830 (tpp) REVERT: D 408 MET cc_start: 0.9128 (tpp) cc_final: 0.8425 (tpp) REVERT: D 455 MET cc_start: 0.9085 (tmm) cc_final: 0.8556 (tmm) REVERT: D 723 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8401 (mp0) outliers start: 54 outliers final: 35 residues processed: 155 average time/residue: 0.2963 time to fit residues: 77.7569 Evaluate side-chains 147 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 168 TRP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 503 TRP Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 723 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 105 optimal weight: 10.0000 chunk 234 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 230 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN D 340 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.052702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.036290 restraints weight = 135650.085| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 4.71 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22192 Z= 0.311 Angle : 0.663 11.121 30182 Z= 0.318 Chirality : 0.044 0.286 3384 Planarity : 0.004 0.036 3770 Dihedral : 10.454 101.052 3511 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.74 % Allowed : 17.47 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.17), residues: 2634 helix: 2.16 (0.13), residues: 1648 sheet: -1.21 (0.84), residues: 40 loop : -0.69 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 509 HIS 0.008 0.001 HIS B 374 PHE 0.013 0.001 PHE C 295 TYR 0.037 0.001 TYR A 21 ARG 0.004 0.000 ARG C 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 105 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.9232 (OUTLIER) cc_final: 0.8980 (t) REVERT: A 402 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9106 (mp) REVERT: A 450 MET cc_start: 0.7974 (tmm) cc_final: 0.7413 (tmm) REVERT: B 332 MET cc_start: 0.7611 (ptt) cc_final: 0.6979 (ptt) REVERT: B 375 GLU cc_start: 0.9500 (OUTLIER) cc_final: 0.9299 (mm-30) REVERT: B 376 MET cc_start: 0.9392 (tpt) cc_final: 0.8695 (tpt) REVERT: B 408 MET cc_start: 0.9667 (mmm) cc_final: 0.8937 (tpp) REVERT: B 455 MET cc_start: 0.9083 (tmm) cc_final: 0.8439 (tmm) REVERT: B 470 LYS cc_start: 0.9350 (OUTLIER) cc_final: 0.8729 (ttmm) REVERT: B 640 MET cc_start: 0.9384 (mmm) cc_final: 0.9071 (tpp) REVERT: B 651 MET cc_start: 0.9323 (mmm) cc_final: 0.8963 (mmm) REVERT: B 723 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: C 91 SER cc_start: 0.9068 (OUTLIER) cc_final: 0.8785 (t) REVERT: C 189 THR cc_start: 0.7314 (OUTLIER) cc_final: 0.6921 (p) REVERT: C 463 TYR cc_start: 0.8794 (t80) cc_final: 0.8260 (t80) REVERT: D 332 MET cc_start: 0.9308 (tpp) cc_final: 0.8964 (tpp) REVERT: D 408 MET cc_start: 0.9144 (tpp) cc_final: 0.8450 (tpp) REVERT: D 455 MET cc_start: 0.9112 (tmm) cc_final: 0.8445 (tmm) REVERT: D 723 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8376 (mp0) outliers start: 63 outliers final: 41 residues processed: 159 average time/residue: 0.2981 time to fit residues: 79.3787 Evaluate side-chains 153 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 104 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 753 ILE Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 TRP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 542 CYS Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 744 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 62 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.053299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.036979 restraints weight = 135949.065| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 4.70 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22192 Z= 0.184 Angle : 0.623 11.598 30182 Z= 0.293 Chirality : 0.042 0.330 3384 Planarity : 0.003 0.036 3770 Dihedral : 9.851 99.525 3511 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.53 % Allowed : 17.73 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.17), residues: 2634 helix: 2.19 (0.13), residues: 1656 sheet: -1.18 (0.83), residues: 40 loop : -0.69 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 509 HIS 0.007 0.001 HIS B 374 PHE 0.021 0.001 PHE B 746 TYR 0.033 0.001 TYR A 21 ARG 0.003 0.000 ARG B 678 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5268 Ramachandran restraints generated. 2634 Oldfield, 0 Emsley, 2634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 108 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 SER cc_start: 0.9196 (OUTLIER) cc_final: 0.8956 (t) REVERT: A 385 MET cc_start: 0.9419 (mmt) cc_final: 0.8990 (mmp) REVERT: A 450 MET cc_start: 0.7923 (tmm) cc_final: 0.7299 (tmm) REVERT: B 332 MET cc_start: 0.7400 (ptt) cc_final: 0.7037 (ptt) REVERT: B 375 GLU cc_start: 0.9550 (OUTLIER) cc_final: 0.9324 (mm-30) REVERT: B 376 MET cc_start: 0.9408 (tpt) cc_final: 0.8700 (tpt) REVERT: B 408 MET cc_start: 0.9662 (mmm) cc_final: 0.8908 (tpp) REVERT: B 455 MET cc_start: 0.9072 (tmm) cc_final: 0.8499 (tmm) REVERT: B 640 MET cc_start: 0.9402 (mmm) cc_final: 0.9066 (tpp) REVERT: B 651 MET cc_start: 0.9366 (mmm) cc_final: 0.9003 (mmm) REVERT: B 723 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: C 91 SER cc_start: 0.9061 (OUTLIER) cc_final: 0.8754 (t) REVERT: C 189 THR cc_start: 0.7322 (OUTLIER) cc_final: 0.6925 (p) REVERT: C 463 TYR cc_start: 0.8764 (t80) cc_final: 0.8177 (t80) REVERT: C 527 ASP cc_start: 0.9547 (OUTLIER) cc_final: 0.9243 (m-30) REVERT: D 332 MET cc_start: 0.9338 (tpp) cc_final: 0.8958 (tpp) REVERT: D 408 MET cc_start: 0.9153 (tpp) cc_final: 0.8415 (tpp) REVERT: D 455 MET cc_start: 0.9117 (tmm) cc_final: 0.8575 (tmm) REVERT: D 651 MET cc_start: 0.9388 (mmm) cc_final: 0.9030 (mmm) REVERT: D 723 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8254 (mp0) outliers start: 58 outliers final: 42 residues processed: 157 average time/residue: 0.3014 time to fit residues: 78.7237 Evaluate side-chains 157 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 108 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 TYR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 430 LYS Chi-restraints excluded: chain A residue 463 TYR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 133 CYS Chi-restraints excluded: chain B residue 203 TRP Chi-restraints excluded: chain B residue 271 TRP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 375 GLU Chi-restraints excluded: chain B residue 470 LYS Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain C residue 21 TYR Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 168 TRP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 184 CYS Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain C residue 482 TYR Chi-restraints excluded: chain C residue 527 ASP Chi-restraints excluded: chain D residue 32 PHE Chi-restraints excluded: chain D residue 133 CYS Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 755 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.5674 > 50: distance: 76 - 95: 9.274 distance: 91 - 95: 5.648 distance: 95 - 96: 13.238 distance: 96 - 97: 19.648 distance: 96 - 99: 29.208 distance: 97 - 98: 29.626 distance: 97 - 106: 32.208 distance: 99 - 100: 26.478 distance: 100 - 101: 12.074 distance: 101 - 102: 9.055 distance: 102 - 103: 9.575 distance: 103 - 104: 11.354 distance: 103 - 105: 12.806 distance: 106 - 107: 18.222 distance: 107 - 108: 23.940 distance: 107 - 110: 21.844 distance: 108 - 109: 12.085 distance: 108 - 114: 52.215 distance: 110 - 111: 36.591 distance: 111 - 112: 41.548 distance: 111 - 113: 40.574 distance: 114 - 115: 27.041 distance: 115 - 116: 40.922 distance: 116 - 117: 44.436 distance: 118 - 119: 28.825 distance: 119 - 120: 22.852 distance: 119 - 122: 43.964 distance: 120 - 127: 14.769 distance: 122 - 123: 39.791 distance: 123 - 124: 35.063 distance: 124 - 125: 21.021 distance: 125 - 126: 25.591 distance: 127 - 128: 19.846 distance: 128 - 129: 12.439 distance: 128 - 131: 39.591 distance: 129 - 130: 45.216 distance: 129 - 133: 18.669 distance: 131 - 132: 9.851 distance: 133 - 134: 20.619 distance: 134 - 135: 19.291 distance: 134 - 137: 32.425 distance: 135 - 136: 21.921 distance: 135 - 142: 21.621 distance: 137 - 138: 20.947 distance: 138 - 139: 24.092 distance: 139 - 140: 11.676 distance: 139 - 141: 20.311 distance: 142 - 143: 8.671 distance: 142 - 148: 4.944 distance: 143 - 144: 22.287 distance: 143 - 146: 11.344 distance: 144 - 145: 18.580 distance: 144 - 149: 13.826 distance: 145 - 178: 17.206 distance: 146 - 147: 18.563 distance: 147 - 148: 17.480 distance: 149 - 150: 20.470 distance: 150 - 151: 12.261 distance: 150 - 153: 4.367 distance: 151 - 152: 16.880 distance: 151 - 163: 17.226 distance: 152 - 183: 24.932 distance: 153 - 154: 17.471 distance: 154 - 155: 10.049 distance: 154 - 156: 19.630 distance: 155 - 157: 12.504 distance: 156 - 158: 11.626 distance: 156 - 159: 6.644 distance: 157 - 158: 9.515 distance: 158 - 160: 14.837 distance: 159 - 161: 24.432 distance: 160 - 162: 14.359 distance: 161 - 162: 13.326 distance: 163 - 164: 12.345 distance: 164 - 165: 15.232 distance: 164 - 167: 19.914 distance: 165 - 166: 15.628 distance: 165 - 170: 21.714 distance: 166 - 190: 25.169 distance: 167 - 168: 7.291 distance: 167 - 169: 41.675 distance: 170 - 171: 20.864 distance: 171 - 172: 4.814 distance: 171 - 174: 24.141 distance: 172 - 173: 22.068 distance: 172 - 178: 8.986 distance: 173 - 197: 26.317 distance: 174 - 175: 6.838 distance: 175 - 176: 21.241 distance: 175 - 177: 15.539