Starting phenix.real_space_refine on Mon Jul 6 08:37:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zgc_60075/07_2026/8zgc_60075.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zgc_60075/07_2026/8zgc_60075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zgc_60075/07_2026/8zgc_60075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zgc_60075/07_2026/8zgc_60075.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zgc_60075/07_2026/8zgc_60075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zgc_60075/07_2026/8zgc_60075.map" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 sd= 0.056 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: 7 Type Number sf(0) Gaussians Mn 6 7.51 5 Fe 2 7.16 5 P 12 5.49 5 S 100 5.16 5 C 21218 2.51 5 N 6304 2.21 5 O 6568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34210 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5756 Classifications: {'peptide': 706} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 662} Chain: "B" Number of atoms: 5756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5756 Classifications: {'peptide': 706} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 662} Chain: "U" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4801 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 549} Chain: "V" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4801 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 549} Chain: "C" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 3476 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 620} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 662} Unresolved chain link angles: 43 Unresolved non-hydrogen bonds: 2449 Unresolved non-hydrogen angles: 3176 Unresolved non-hydrogen dihedrals: 2099 Unresolved non-hydrogen chiralities: 183 Planarities with less than four sites: {'ASN:plan1': 26, 'GLU:plan': 49, 'TYR:plan': 32, 'ARG:plan': 50, 'PHE:plan': 36, 'TRP:plan': 17, 'ASP:plan': 47, 'GLN:plan1': 29, 'HIS:plan': 23} Unresolved non-hydrogen planarities: 1489 Chain: "D" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 3476 Classifications: {'peptide': 706} Incomplete info: {'truncation_to_alanine': 620} Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 662} Unresolved chain link angles: 43 Unresolved non-hydrogen bonds: 2449 Unresolved non-hydrogen angles: 3176 Unresolved non-hydrogen dihedrals: 2099 Unresolved non-hydrogen chiralities: 183 Planarities with less than four sites: {'ASN:plan1': 26, 'GLU:plan': 49, 'TYR:plan': 32, 'ARG:plan': 50, 'PHE:plan': 36, 'TRP:plan': 17, 'ASP:plan': 47, 'GLN:plan1': 29, 'HIS:plan': 23} Unresolved non-hydrogen planarities: 1489 Chain: "W" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 2916 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 518} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 549} Unresolved chain link angles: 37 Unresolved non-hydrogen bonds: 2014 Unresolved non-hydrogen angles: 2583 Unresolved non-hydrogen dihedrals: 1729 Unresolved non-hydrogen chiralities: 143 Planarities with less than four sites: {'TYR:plan': 24, 'PHE:plan': 23, 'GLU:plan': 44, 'ARG:plan': 49, 'TRP:plan': 13, 'GLN:plan1': 19, 'ASN:plan1': 18, 'HIS:plan': 19, 'ASP:plan': 38} Unresolved non-hydrogen planarities: 1183 Chain: "X" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 2916 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 518} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 549} Unresolved chain link angles: 37 Unresolved non-hydrogen bonds: 2014 Unresolved non-hydrogen angles: 2583 Unresolved non-hydrogen dihedrals: 1729 Unresolved non-hydrogen chiralities: 143 Planarities with less than four sites: {'TYR:plan': 24, 'PHE:plan': 23, 'GLU:plan': 44, 'ARG:plan': 49, 'TRP:plan': 13, 'GLN:plan1': 19, 'ASN:plan1': 18, 'HIS:plan': 19, 'ASP:plan': 38} Unresolved non-hydrogen planarities: 1183 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: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Ad-hoc single atom residues: {'FE2': 1, ' MN': 1} Unusual residues: {'AKG': 1, 'NAG': 2, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 63 Ad-hoc single atom residues: {'FE2': 1, ' MN': 1} Unusual residues: {'AKG': 1, 'NAG': 2, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'GDU': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Chain: "V" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 61 Ad-hoc single atom residues: {' MN': 2} Unusual residues: {'GDU': 1, 'UDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Time building chain proxies: 8.33, per 1000 atoms: 0.24 Number of scatterers: 34210 At special positions: 0 Unit cell: (178.2, 226.6, 238.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 Mn 6 24.99 S 100 16.00 P 12 15.00 O 6568 8.00 N 6304 7.00 C 21218 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 385 " distance=2.04 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 698 " distance=2.03 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 282 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 385 " distance=2.04 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 698 " distance=2.03 Simple disulfide: pdb=" SG CYS U 228 " - pdb=" SG CYS U 283 " distance=2.03 Simple disulfide: pdb=" SG CYS V 228 " - pdb=" SG CYS V 283 " distance=2.06 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-ASN " NAG A 801 " - " ASN A 63 " " NAG A 802 " - " ASN A 548 " " NAG B 801 " - " ASN B 63 " " NAG B 802 " - " ASN B 548 " " NAG E 1 " - " ASN U 184 " " NAG F 1 " - " ASN V 184 " Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.7 seconds 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9760 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 60 sheets defined 34.0% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 49 through 62 removed outlier: 3.926A pdb=" N PHE A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 97 Processing helix chain 'A' and resid 98 through 101 removed outlier: 3.860A pdb=" N ALA A 101 " --> pdb=" O GLU A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 98 through 101' Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 148 through 154 removed outlier: 3.927A pdb=" N GLU A 152 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 182 removed outlier: 4.369A pdb=" N GLN A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 201 removed outlier: 3.675A pdb=" N ASP A 201 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 225 through 229 removed outlier: 4.101A pdb=" N VAL A 229 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 266 Processing helix chain 'A' and resid 289 through 293 removed outlier: 4.531A pdb=" N GLY A 292 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN A 293 " --> pdb=" O PRO A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 293' Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 339 through 354 Proline residue: A 348 - end of helix Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.534A pdb=" N GLU A 364 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.921A pdb=" N ASN A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 removed outlier: 3.778A pdb=" N GLN A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 488 through 500 removed outlier: 3.541A pdb=" N LYS A 500 " --> pdb=" O SER A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 536 through 545 Processing helix chain 'A' and resid 548 through 555 Processing helix chain 'A' and resid 573 through 588 Processing helix chain 'A' and resid 614 through 618 Processing helix chain 'A' and resid 619 through 631 removed outlier: 3.503A pdb=" N VAL A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 639 Processing helix chain 'B' and resid 49 through 62 removed outlier: 3.606A pdb=" N LEU B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 62 " --> pdb=" O SER B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 98 removed outlier: 4.599A pdb=" N VAL B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 121 through 133 Processing helix chain 'B' and resid 148 through 154 removed outlier: 4.102A pdb=" N GLU B 152 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR B 154 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.907A pdb=" N ASP B 201 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 258 through 266 removed outlier: 3.761A pdb=" N LEU B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 318 Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 339 through 354 removed outlier: 3.515A pdb=" N ILE B 343 " --> pdb=" O HIS B 339 " (cutoff:3.500A) Proline residue: B 348 - end of helix Processing helix chain 'B' and resid 367 through 382 Processing helix chain 'B' and resid 401 through 410 removed outlier: 4.103A pdb=" N ASN B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 Processing helix chain 'B' and resid 468 through 475 removed outlier: 3.613A pdb=" N LEU B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 499 Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 536 through 544 Processing helix chain 'B' and resid 548 through 555 Processing helix chain 'B' and resid 573 through 588 removed outlier: 3.653A pdb=" N TYR B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B 588 " --> pdb=" O MET B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 618 Processing helix chain 'B' and resid 619 through 630 Processing helix chain 'B' and resid 630 through 639 removed outlier: 3.845A pdb=" N MET B 634 " --> pdb=" O TYR B 630 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 75 Processing helix chain 'U' and resid 96 through 107 removed outlier: 3.527A pdb=" N VAL U 100 " --> pdb=" O ASN U 96 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 152 removed outlier: 3.513A pdb=" N TYR U 140 " --> pdb=" O SER U 136 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU U 141 " --> pdb=" O ASP U 137 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N HIS U 142 " --> pdb=" O SER U 138 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS U 145 " --> pdb=" O GLU U 141 " (cutoff:3.500A) Processing helix chain 'U' and resid 175 through 182 Processing helix chain 'U' and resid 217 through 222 Processing helix chain 'U' and resid 244 through 249 removed outlier: 3.933A pdb=" N ASN U 249 " --> pdb=" O ALA U 246 " (cutoff:3.500A) Processing helix chain 'U' and resid 266 through 273 Processing helix chain 'U' and resid 300 through 317 removed outlier: 3.632A pdb=" N GLU U 304 " --> pdb=" O THR U 300 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET U 316 " --> pdb=" O GLN U 312 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL U 317 " --> pdb=" O LEU U 313 " (cutoff:3.500A) Processing helix chain 'U' and resid 352 through 365 removed outlier: 3.754A pdb=" N GLU U 356 " --> pdb=" O GLN U 352 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG U 357 " --> pdb=" O ASP U 353 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET U 358 " --> pdb=" O ARG U 354 " (cutoff:3.500A) Processing helix chain 'U' and resid 381 through 386 Processing helix chain 'U' and resid 387 through 389 No H-bonds generated for 'chain 'U' and resid 387 through 389' Processing helix chain 'U' and resid 407 through 427 Processing helix chain 'U' and resid 443 through 459 Processing helix chain 'U' and resid 503 through 513 removed outlier: 3.926A pdb=" N GLU U 513 " --> pdb=" O LEU U 509 " (cutoff:3.500A) Processing helix chain 'U' and resid 520 through 529 Proline residue: U 526 - end of helix removed outlier: 3.972A pdb=" N PHE U 529 " --> pdb=" O LEU U 525 " (cutoff:3.500A) Processing helix chain 'U' and resid 534 through 541 removed outlier: 3.978A pdb=" N LYS U 538 " --> pdb=" O VAL U 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 76 removed outlier: 3.846A pdb=" N ARG V 76 " --> pdb=" O GLY V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 80 through 83 Processing helix chain 'V' and resid 96 through 109 Processing helix chain 'V' and resid 136 through 154 Processing helix chain 'V' and resid 175 through 182 Processing helix chain 'V' and resid 217 through 222 Processing helix chain 'V' and resid 244 through 249 removed outlier: 3.617A pdb=" N ASN V 249 " --> pdb=" O ALA V 246 " (cutoff:3.500A) Processing helix chain 'V' and resid 267 through 276 Processing helix chain 'V' and resid 300 through 317 removed outlier: 3.549A pdb=" N GLU V 304 " --> pdb=" O THR V 300 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET V 316 " --> pdb=" O GLN V 312 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL V 317 " --> pdb=" O LEU V 313 " (cutoff:3.500A) Processing helix chain 'V' and resid 352 through 365 removed outlier: 3.767A pdb=" N GLU V 356 " --> pdb=" O GLN V 352 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG V 357 " --> pdb=" O ASP V 353 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET V 358 " --> pdb=" O ARG V 354 " (cutoff:3.500A) Processing helix chain 'V' and resid 381 through 386 Processing helix chain 'V' and resid 387 through 389 No H-bonds generated for 'chain 'V' and resid 387 through 389' Processing helix chain 'V' and resid 407 through 427 Processing helix chain 'V' and resid 443 through 459 Processing helix chain 'V' and resid 503 through 513 Processing helix chain 'V' and resid 520 through 528 Proline residue: V 526 - end of helix Processing helix chain 'V' and resid 534 through 541 removed outlier: 4.068A pdb=" N LYS V 538 " --> pdb=" O VAL V 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 49 through 62 Processing helix chain 'C' and resid 86 through 98 removed outlier: 3.856A pdb=" N VAL C 90 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 121 through 133 Processing helix chain 'C' and resid 147 through 153 removed outlier: 3.839A pdb=" N GLU C 152 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 Processing helix chain 'C' and resid 190 through 201 Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 258 through 267 Processing helix chain 'C' and resid 310 through 319 removed outlier: 3.502A pdb=" N LEU C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 339 through 354 Proline residue: C 348 - end of helix Processing helix chain 'C' and resid 361 through 365 Processing helix chain 'C' and resid 367 through 382 Processing helix chain 'C' and resid 401 through 409 Processing helix chain 'C' and resid 443 through 449 Processing helix chain 'C' and resid 469 through 475 Processing helix chain 'C' and resid 488 through 500 Processing helix chain 'C' and resid 527 through 534 removed outlier: 4.058A pdb=" N ILE C 533 " --> pdb=" O LEU C 530 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE C 534 " --> pdb=" O TRP C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'C' and resid 548 through 554 Processing helix chain 'C' and resid 573 through 588 Processing helix chain 'C' and resid 619 through 630 Processing helix chain 'C' and resid 630 through 639 removed outlier: 3.541A pdb=" N MET C 634 " --> pdb=" O TYR C 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 49 through 62 Processing helix chain 'D' and resid 86 through 98 removed outlier: 3.541A pdb=" N VAL D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 121 through 133 removed outlier: 3.523A pdb=" N GLY D 133 " --> pdb=" O PHE D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 removed outlier: 3.824A pdb=" N GLU D 152 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 190 through 201 removed outlier: 3.592A pdb=" N PHE D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 258 through 267 removed outlier: 3.548A pdb=" N ASN D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 339 through 354 Proline residue: D 348 - end of helix Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 367 through 382 Processing helix chain 'D' and resid 401 through 409 Processing helix chain 'D' and resid 443 through 449 Processing helix chain 'D' and resid 469 through 475 Processing helix chain 'D' and resid 488 through 500 Processing helix chain 'D' and resid 527 through 534 removed outlier: 4.036A pdb=" N ILE D 533 " --> pdb=" O LEU D 530 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE D 534 " --> pdb=" O TRP D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 545 Processing helix chain 'D' and resid 548 through 554 Processing helix chain 'D' and resid 573 through 588 Processing helix chain 'D' and resid 619 through 630 Processing helix chain 'D' and resid 630 through 639 removed outlier: 3.599A pdb=" N MET D 634 " --> pdb=" O TYR D 630 " (cutoff:3.500A) Processing helix chain 'W' and resid 66 through 76 removed outlier: 3.523A pdb=" N ARG W 76 " --> pdb=" O GLY W 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 82 No H-bonds generated for 'chain 'W' and resid 80 through 82' Processing helix chain 'W' and resid 96 through 109 Processing helix chain 'W' and resid 136 through 157 removed outlier: 3.584A pdb=" N MET W 157 " --> pdb=" O SER W 153 " (cutoff:3.500A) Processing helix chain 'W' and resid 175 through 183 Processing helix chain 'W' and resid 216 through 222 Processing helix chain 'W' and resid 244 through 250 Processing helix chain 'W' and resid 264 through 276 Processing helix chain 'W' and resid 300 through 319 removed outlier: 4.021A pdb=" N LYS W 318 " --> pdb=" O GLU W 314 " (cutoff:3.500A) Processing helix chain 'W' and resid 352 through 365 Processing helix chain 'W' and resid 376 through 380 Processing helix chain 'W' and resid 381 through 388 Processing helix chain 'W' and resid 406 through 427 Processing helix chain 'W' and resid 443 through 459 Processing helix chain 'W' and resid 503 through 512 Processing helix chain 'W' and resid 513 through 517 removed outlier: 4.063A pdb=" N SER W 516 " --> pdb=" O GLU W 513 " (cutoff:3.500A) Processing helix chain 'W' and resid 520 through 529 Proline residue: W 526 - end of helix Processing helix chain 'W' and resid 534 through 540 removed outlier: 3.585A pdb=" N LYS W 538 " --> pdb=" O VAL W 534 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 76 Processing helix chain 'X' and resid 80 through 84 Processing helix chain 'X' and resid 96 through 109 Processing helix chain 'X' and resid 136 through 157 Processing helix chain 'X' and resid 175 through 183 removed outlier: 3.683A pdb=" N GLU X 183 " --> pdb=" O LEU X 179 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 222 Processing helix chain 'X' and resid 244 through 250 Processing helix chain 'X' and resid 264 through 276 removed outlier: 3.600A pdb=" N PHE X 269 " --> pdb=" O ASP X 265 " (cutoff:3.500A) Processing helix chain 'X' and resid 300 through 319 removed outlier: 3.970A pdb=" N LYS X 318 " --> pdb=" O GLU X 314 " (cutoff:3.500A) Processing helix chain 'X' and resid 352 through 365 Processing helix chain 'X' and resid 376 through 380 Processing helix chain 'X' and resid 381 through 388 Processing helix chain 'X' and resid 406 through 427 Processing helix chain 'X' and resid 443 through 459 Processing helix chain 'X' and resid 503 through 512 Processing helix chain 'X' and resid 513 through 518 removed outlier: 4.023A pdb=" N MET X 518 " --> pdb=" O LEU X 515 " (cutoff:3.500A) Processing helix chain 'X' and resid 520 through 529 Proline residue: X 526 - end of helix Processing helix chain 'X' and resid 534 through 540 removed outlier: 3.562A pdb=" N LYS X 538 " --> pdb=" O VAL X 534 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 69 removed outlier: 8.217A pdb=" N ARG A 67 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL A 41 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU A 69 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR A 43 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 109 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A 44 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE A 163 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 141 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER A 139 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N GLY A 167 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N LEU A 137 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU A 136 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASP A 213 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N PHE A 138 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.588A pdb=" N ILE A 117 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL A 252 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 230 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 329 removed outlier: 6.947A pdb=" N VAL A 298 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE A 299 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 465 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 302 through 304 removed outlier: 6.409A pdb=" N VAL A 302 " --> pdb=" O HIS A 333 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 396 through 397 Processing sheet with id=AA7, first strand: chain 'A' and resid 455 through 457 Processing sheet with id=AA8, first strand: chain 'A' and resid 567 through 570 removed outlier: 5.733A pdb=" N TRP A 707 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 678 " --> pdb=" O TRP A 707 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS A 711 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE A 673 " --> pdb=" O VAL A 736 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 736 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N MET A 650 " --> pdb=" O PHE A 735 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 612 " --> pdb=" O VAL A 653 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB1, first strand: chain 'A' and resid 698 through 699 Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 67 removed outlier: 8.194A pdb=" N ARG B 67 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N VAL B 41 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N GLY B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 11.632A pdb=" N LEU B 137 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AB4, first strand: chain 'B' and resid 229 through 233 Processing sheet with id=AB5, first strand: chain 'B' and resid 328 through 329 removed outlier: 7.148A pdb=" N VAL B 298 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 328 through 329 removed outlier: 7.148A pdb=" N VAL B 298 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N PHE B 299 " --> pdb=" O PHE B 389 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LEU B 391 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA B 301 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B 465 " --> pdb=" O SER B 390 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 431 through 432 Processing sheet with id=AB8, first strand: chain 'B' and resid 455 through 458 removed outlier: 4.098A pdb=" N LEU B 504 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 567 through 570 removed outlier: 5.511A pdb=" N TRP B 707 " --> pdb=" O ALA B 678 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 678 " --> pdb=" O TRP B 707 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS B 711 " --> pdb=" O THR B 674 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE B 673 " --> pdb=" O VAL B 736 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B 736 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET B 650 " --> pdb=" O PHE B 735 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 653 " --> pdb=" O ILE B 612 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 686 through 687 Processing sheet with id=AC2, first strand: chain 'B' and resid 698 through 699 Processing sheet with id=AC3, first strand: chain 'U' and resid 115 through 117 removed outlier: 9.061A pdb=" N GLU U 116 " --> pdb=" O THR U 84 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU U 86 " --> pdb=" O GLU U 116 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU U 58 " --> pdb=" O TRP U 87 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA U 89 " --> pdb=" O LEU U 58 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA U 60 " --> pdb=" O ALA U 89 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU U 55 " --> pdb=" O LEU U 163 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE U 238 " --> pdb=" O PHE U 164 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL U 187 " --> pdb=" O TYR U 281 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N CYS U 283 " --> pdb=" O VAL U 187 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA U 189 " --> pdb=" O CYS U 283 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N MET U 280 " --> pdb=" O VAL U 231 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'U' and resid 170 through 171 Processing sheet with id=AC5, first strand: chain 'U' and resid 342 through 343 removed outlier: 6.631A pdb=" N GLU U 342 " --> pdb=" O LEU U 432 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR U 499 " --> pdb=" O VAL U 433 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE U 549 " --> pdb=" O LEU U 464 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'U' and resid 346 through 347 removed outlier: 3.894A pdb=" N ASN U 347 " --> pdb=" O VAL U 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'U' and resid 439 through 440 Processing sheet with id=AC8, first strand: chain 'V' and resid 114 through 117 removed outlier: 3.535A pdb=" N VAL V 88 " --> pdb=" O GLU V 116 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU V 55 " --> pdb=" O LEU V 163 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE V 238 " --> pdb=" O PHE V 164 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL V 187 " --> pdb=" O TYR V 281 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N CYS V 283 " --> pdb=" O VAL V 187 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA V 189 " --> pdb=" O CYS V 283 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N MET V 280 " --> pdb=" O VAL V 231 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL V 282 " --> pdb=" O PHE V 229 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'V' and resid 342 through 345 removed outlier: 4.234A pdb=" N GLU V 342 " --> pdb=" O LYS V 430 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL V 433 " --> pdb=" O TYR V 499 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR V 499 " --> pdb=" O VAL V 433 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TYR V 494 " --> pdb=" O ARG V 471 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG V 471 " --> pdb=" O TYR V 494 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR V 496 " --> pdb=" O ARG V 469 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ARG V 469 " --> pdb=" O THR V 496 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA V 498 " --> pdb=" O VAL V 467 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL V 467 " --> pdb=" O ALA V 498 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE V 465 " --> pdb=" O VAL V 500 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 439 through 440 removed outlier: 3.647A pdb=" N TYR V 557 " --> pdb=" O ARG V 439 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 487 through 489 Processing sheet with id=AD3, first strand: chain 'C' and resid 66 through 69 removed outlier: 8.363A pdb=" N ARG C 67 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C 41 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU C 69 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N THR C 43 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL C 44 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE C 169 " --> pdb=" O PHE C 110 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP C 112 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N GLY C 167 " --> pdb=" O ASP C 112 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE C 163 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N GLY C 167 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 11.546A pdb=" N LEU C 137 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU C 136 " --> pdb=" O ASN C 211 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 116 through 118 Processing sheet with id=AD5, first strand: chain 'C' and resid 229 through 233 Processing sheet with id=AD6, first strand: chain 'C' and resid 356 through 360 removed outlier: 4.192A pdb=" N ALA C 356 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C 303 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA C 464 " --> pdb=" O PRO C 416 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU C 504 " --> pdb=" O VAL C 458 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 395 through 396 Processing sheet with id=AD8, first strand: chain 'C' and resid 428 through 429 removed outlier: 4.101A pdb=" N TRP C 429 " --> pdb=" O TYR C 460 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR C 460 " --> pdb=" O TRP C 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 431 through 432 Processing sheet with id=AE1, first strand: chain 'C' and resid 560 through 563 removed outlier: 5.510A pdb=" N GLN C 561 " --> pdb=" O TRP C 568 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N TRP C 568 " --> pdb=" O GLN C 561 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS C 563 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N TRP C 707 " --> pdb=" O ALA C 678 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA C 678 " --> pdb=" O TRP C 707 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE C 673 " --> pdb=" O VAL C 736 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET C 650 " --> pdb=" O PHE C 735 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 664 through 667 removed outlier: 5.747A pdb=" N ARG C 665 " --> pdb=" O GLY C 721 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLY C 721 " --> pdb=" O ARG C 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 686 through 688 Processing sheet with id=AE4, first strand: chain 'D' and resid 66 through 69 removed outlier: 8.196A pdb=" N ARG D 67 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL D 41 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU D 69 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR D 43 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL D 44 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 169 " --> pdb=" O PHE D 110 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP D 112 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N GLY D 167 " --> pdb=" O ASP D 112 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N GLY D 167 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 11.453A pdb=" N LEU D 137 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU D 136 " --> pdb=" O ASN D 211 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 116 through 118 Processing sheet with id=AE6, first strand: chain 'D' and resid 229 through 233 Processing sheet with id=AE7, first strand: chain 'D' and resid 356 through 360 removed outlier: 4.104A pdb=" N ALA D 356 " --> pdb=" O VAL D 328 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG D 297 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE D 389 " --> pdb=" O ARG D 297 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE D 299 " --> pdb=" O PHE D 389 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU D 391 " --> pdb=" O PHE D 299 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ALA D 301 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA D 464 " --> pdb=" O PRO D 416 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL D 413 " --> pdb=" O HIS D 505 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N SER D 507 " --> pdb=" O VAL D 413 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA D 415 " --> pdb=" O SER D 507 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU D 504 " --> pdb=" O VAL D 458 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 396 through 397 Processing sheet with id=AE9, first strand: chain 'D' and resid 428 through 429 removed outlier: 3.721A pdb=" N TRP D 429 " --> pdb=" O TYR D 460 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR D 460 " --> pdb=" O TRP D 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'D' and resid 431 through 432 removed outlier: 4.085A pdb=" N ALA D 431 " --> pdb=" O ALA D 439 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA D 439 " --> pdb=" O ALA D 431 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 560 through 563 removed outlier: 7.152A pdb=" N VAL D 566 " --> pdb=" O PRO D 562 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TRP D 707 " --> pdb=" O ALA D 678 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA D 678 " --> pdb=" O TRP D 707 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS D 711 " --> pdb=" O THR D 674 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET D 650 " --> pdb=" O PHE D 735 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 664 through 667 removed outlier: 5.578A pdb=" N ARG D 665 " --> pdb=" O GLY D 721 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLY D 721 " --> pdb=" O ARG D 665 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS D 719 " --> pdb=" O HIS D 667 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N CYS D 691 " --> pdb=" O ILE D 700 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 686 through 687 Processing sheet with id=AF5, first strand: chain 'W' and resid 114 through 115 removed outlier: 4.042A pdb=" N SER W 114 " --> pdb=" O THR W 84 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ALA W 89 " --> pdb=" O ILE W 56 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU W 58 " --> pdb=" O ALA W 89 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASP W 91 " --> pdb=" O LEU W 58 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA W 60 " --> pdb=" O ASP W 91 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR W 90 " --> pdb=" O ALA W 120 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'W' and resid 114 through 115 removed outlier: 4.042A pdb=" N SER W 114 " --> pdb=" O THR W 84 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU W 55 " --> pdb=" O LEU W 163 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL W 165 " --> pdb=" O LEU W 55 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA W 57 " --> pdb=" O VAL W 165 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE W 238 " --> pdb=" O PHE W 164 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'W' and resid 192 through 193 Processing sheet with id=AF8, first strand: chain 'W' and resid 201 through 202 Processing sheet with id=AF9, first strand: chain 'W' and resid 370 through 373 removed outlier: 6.054A pdb=" N VAL W 343 " --> pdb=" O ARG W 370 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL W 372 " --> pdb=" O VAL W 343 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N MET W 345 " --> pdb=" O VAL W 372 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU W 342 " --> pdb=" O LYS W 430 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR W 499 " --> pdb=" O VAL W 433 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR W 496 " --> pdb=" O GLY W 468 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY W 468 " --> pdb=" O THR W 496 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ALA W 498 " --> pdb=" O TYR W 466 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR W 466 " --> pdb=" O ALA W 498 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 438 through 440 Processing sheet with id=AG2, first strand: chain 'W' and resid 487 through 489 Processing sheet with id=AG3, first strand: chain 'X' and resid 118 through 119 removed outlier: 3.736A pdb=" N THR X 90 " --> pdb=" O ARG X 118 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ALA X 89 " --> pdb=" O ILE X 56 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU X 58 " --> pdb=" O ALA X 89 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU X 59 " --> pdb=" O VAL X 165 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL X 187 " --> pdb=" O TYR X 281 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N CYS X 283 " --> pdb=" O VAL X 187 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ALA X 189 " --> pdb=" O CYS X 283 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 201 through 202 removed outlier: 3.686A pdb=" N MET X 233 " --> pdb=" O TRP X 202 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 370 through 372 removed outlier: 5.884A pdb=" N VAL X 343 " --> pdb=" O ARG X 370 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL X 372 " --> pdb=" O VAL X 343 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N MET X 345 " --> pdb=" O VAL X 372 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU X 342 " --> pdb=" O LYS X 430 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER X 431 " --> pdb=" O ILE X 501 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE X 501 " --> pdb=" O SER X 431 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL X 433 " --> pdb=" O TYR X 499 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N TYR X 499 " --> pdb=" O VAL X 433 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N THR X 496 " --> pdb=" O GLY X 468 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N GLY X 468 " --> pdb=" O THR X 496 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N ALA X 498 " --> pdb=" O TYR X 466 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N TYR X 466 " --> pdb=" O ALA X 498 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 487 through 489 1341 hydrogen bonds defined for protein. 3762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.80 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 11050 1.33 - 1.47: 8918 1.47 - 1.60: 14648 1.60 - 1.73: 8 1.73 - 1.86: 172 Bond restraints: 34796 Sorted by residual: bond pdb=" O5' UDP U 702 " pdb=" PA UDP U 702 " ideal model delta sigma weight residual 1.581 1.779 -0.198 1.50e-02 4.44e+03 1.75e+02 bond pdb=" O3A UDP A 805 " pdb=" PB UDP A 805 " ideal model delta sigma weight residual 1.584 1.702 -0.118 1.00e-02 1.00e+04 1.40e+02 bond pdb=" O5' UDP A 805 " pdb=" PA UDP A 805 " ideal model delta sigma weight residual 1.581 1.754 -0.173 1.50e-02 4.44e+03 1.33e+02 bond pdb=" O5' UDP B 805 " pdb=" PA UDP B 805 " ideal model delta sigma weight residual 1.581 1.733 -0.152 1.50e-02 4.44e+03 1.03e+02 bond pdb=" O5' UDP V 702 " pdb=" PA UDP V 702 " ideal model delta sigma weight residual 1.581 1.729 -0.148 1.50e-02 4.44e+03 9.74e+01 ... (remaining 34791 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.44: 47643 6.44 - 12.87: 77 12.87 - 19.31: 2 19.31 - 25.75: 0 25.75 - 32.19: 2 Bond angle restraints: 47724 Sorted by residual: angle pdb=" O5' UDP A 805 " pdb=" PA UDP A 805 " pdb=" O2A UDP A 805 " ideal model delta sigma weight residual 110.83 98.58 12.25 1.00e+00 1.00e+00 1.50e+02 angle pdb=" O5' UDP V 702 " pdb=" PA UDP V 702 " pdb=" O2A UDP V 702 " ideal model delta sigma weight residual 110.83 98.79 12.04 1.00e+00 1.00e+00 1.45e+02 angle pdb=" O1A UDP A 805 " pdb=" PA UDP A 805 " pdb=" O3A UDP A 805 " ideal model delta sigma weight residual 109.95 121.95 -12.00 1.00e+00 1.00e+00 1.44e+02 angle pdb=" O5' UDP B 805 " pdb=" PA UDP B 805 " pdb=" O1A UDP B 805 " ideal model delta sigma weight residual 106.70 95.17 11.53 1.00e+00 1.00e+00 1.33e+02 angle pdb=" O3A UDP A 805 " pdb=" PB UDP A 805 " pdb=" O3B UDP A 805 " ideal model delta sigma weight residual 112.01 101.18 10.83 1.00e+00 1.00e+00 1.17e+02 ... (remaining 47719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 18715 17.96 - 35.93: 1534 35.93 - 53.89: 484 53.89 - 71.86: 97 71.86 - 89.82: 40 Dihedral angle restraints: 20870 sinusoidal: 5834 harmonic: 15036 Sorted by residual: dihedral pdb=" CB CYS B 279 " pdb=" SG CYS B 279 " pdb=" SG CYS B 282 " pdb=" CB CYS B 282 " ideal model delta sinusoidal sigma weight residual -86.00 -14.32 -71.68 1 1.00e+01 1.00e-02 6.58e+01 dihedral pdb=" CA GLN A 306 " pdb=" C GLN A 306 " pdb=" N PRO A 307 " pdb=" CA PRO A 307 " ideal model delta harmonic sigma weight residual 180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CB CYS V 228 " pdb=" SG CYS V 228 " pdb=" SG CYS V 283 " pdb=" CB CYS V 283 " ideal model delta sinusoidal sigma weight residual 93.00 50.76 42.24 1 1.00e+01 1.00e-02 2.49e+01 ... (remaining 20867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4701 0.062 - 0.125: 847 0.125 - 0.187: 43 0.187 - 0.249: 9 0.249 - 0.311: 6 Chirality restraints: 5606 Sorted by residual: chirality pdb=" CA PRO D 270 " pdb=" N PRO D 270 " pdb=" C PRO D 270 " pdb=" CB PRO D 270 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 548 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C1 NAG B 802 " pdb=" ND2 ASN B 548 " pdb=" C2 NAG B 802 " pdb=" O5 NAG B 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 5603 not shown) Planarity restraints: 6462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 801 " -0.231 2.00e-02 2.50e+03 1.92e-01 4.59e+02 pdb=" C7 NAG A 801 " 0.066 2.00e-02 2.50e+03 pdb=" C8 NAG A 801 " -0.164 2.00e-02 2.50e+03 pdb=" N2 NAG A 801 " 0.315 2.00e-02 2.50e+03 pdb=" O7 NAG A 801 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 290 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C PRO C 290 " -0.067 2.00e-02 2.50e+03 pdb=" O PRO C 290 " 0.025 2.00e-02 2.50e+03 pdb=" N GLY C 291 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL X 372 " -0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C VAL X 372 " 0.057 2.00e-02 2.50e+03 pdb=" O VAL X 372 " -0.022 2.00e-02 2.50e+03 pdb=" N GLU X 373 " -0.019 2.00e-02 2.50e+03 ... (remaining 6459 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 966 2.70 - 3.25: 33336 3.25 - 3.80: 50202 3.80 - 4.35: 58895 4.35 - 4.90: 100330 Nonbonded interactions: 243729 Sorted by model distance: nonbonded pdb=" OH TYR U 259 " pdb=" O SER U 262 " model vdw 2.151 3.040 nonbonded pdb=" OG SER A 426 " pdb=" OH TYR A 444 " model vdw 2.159 3.040 nonbonded pdb=" OE2 GLU V 75 " pdb=" NE1 TRP V 104 " model vdw 2.165 3.120 nonbonded pdb=" OE1 GLN A 625 " pdb=" OG1 THR A 629 " model vdw 2.190 3.040 nonbonded pdb=" OD1 ASP B 480 " pdb=" OG SER B 483 " model vdw 2.191 3.040 ... (remaining 243724 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 33 through 50 and (name N or name CA or name C or name O \ or name CB )) or resid 51 or (resid 52 through 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 or (resid 71 and (name N or name CA or na \ me C or name O or name CB )) or resid 72 or (resid 73 through 76 and (name N or \ name CA or name C or name O or name CB )) or resid 77 through 78 or (resid 79 th \ rough 84 and (name N or name CA or name C or name O or name CB )) or resid 85 th \ rough 87 or (resid 88 through 119 and (name N or name CA or name C or name O or \ name CB )) or resid 120 or (resid 121 through 132 and (name N or name CA or name \ C or name O or name CB )) or resid 133 or (resid 134 through 148 and (name N or \ name CA or name C or name O or name CB )) or resid 149 or (resid 150 through 15 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 158 or (resi \ d 159 and (name N or name CA or name C or name O or name CB )) or resid 160 or ( \ resid 161 through 166 and (name N or name CA or name C or name O or name CB )) o \ r resid 167 through 168 or (resid 169 through 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 or (resid 172 through 202 and (name N or \ name CA or name C or name O or name CB )) or resid 203 or (resid 204 through 22 \ 3 and (name N or name CA or name C or name O or name CB )) or (resid 224 through \ 253 and (name N or name CA or name C or name O or name CB )) or resid 254 or (r \ esid 255 and (name N or name CA or name C or name O or name CB )) or resid 256 o \ r (resid 257 through 265 and (name N or name CA or name C or name O or name CB ) \ ) or resid 266 or (resid 267 through 271 and (name N or name CA or name C or nam \ e O or name CB )) or resid 272 or (resid 273 through 276 and (name N or name CA \ or name C or name O or name CB )) or resid 277 through 278 or (resid 279 and (na \ me N or name CA or name C or name O or name CB )) or resid 280 or (resid 281 thr \ ough 290 and (name N or name CA or name C or name O or name CB )) or resid 291 t \ hrough 292 or (resid 293 through 360 and (name N or name CA or name C or name O \ or name CB )) or resid 361 or (resid 362 through 368 and (name N or name CA or n \ ame C or name O or name CB )) or resid 369 or (resid 370 through 421 and (name N \ or name CA or name C or name O or name CB )) or resid 422 or (resid 423 through \ 429 and (name N or name CA or name C or name O or name CB )) or (resid 430 thro \ ugh 453 and (name N or name CA or name C or name O or name CB )) or resid 454 or \ (resid 455 through 468 and (name N or name CA or name C or name O or name CB )) \ or resid 469 or (resid 470 through 483 and (name N or name CA or name C or name \ O or name CB )) or resid 484 or (resid 485 through 500 and (name N or name CA o \ r name C or name O or name CB )) or resid 501 or (resid 502 through 512 and (nam \ e N or name CA or name C or name O or name CB )) or resid 513 or (resid 514 thro \ ugh 554 and (name N or name CA or name C or name O or name CB )) or resid 555 or \ (resid 556 and (name N or name CA or name C or name O or name CB )) or resid 55 \ 7 or (resid 558 through 587 and (name N or name CA or name C or name O or name C \ B )) or resid 588 or (resid 589 through 591 and (name N or name CA or name C or \ name O or name CB )) or resid 592 through 593 or (resid 594 through 601 and (nam \ e N or name CA or name C or name O or name CB )) or resid 602 through 603 or (re \ sid 604 through 617 and (name N or name CA or name C or name O or name CB )) or \ resid 618 or (resid 619 through 631 and (name N or name CA or name C or name O o \ r name CB )) or resid 632 or (resid 633 through 640 and (name N or name CA or na \ me C or name O or name CB )) or resid 641 or (resid 642 through 682 and (name N \ or name CA or name C or name O or name CB )) or resid 683 or (resid 684 through \ 687 and (name N or name CA or name C or name O or name CB )) or resid 688 throug \ h 690 or (resid 691 through 705 and (name N or name CA or name C or name O or na \ me CB )) or resid 706 or (resid 707 through 712 and (name N or name CA or name C \ or name O or name CB )) or resid 713 or (resid 714 through 720 and (name N or n \ ame CA or name C or name O or name CB )) or resid 721 or (resid 722 through 726 \ and (name N or name CA or name C or name O or name CB )) or resid 727 or (resid \ 728 through 738 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and ((resid 33 through 50 and (name N or name CA or name C or name O \ or name CB )) or resid 51 or (resid 52 through 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 or (resid 71 and (name N or name CA or na \ me C or name O or name CB )) or resid 72 or (resid 73 through 76 and (name N or \ name CA or name C or name O or name CB )) or resid 77 through 78 or (resid 79 th \ rough 84 and (name N or name CA or name C or name O or name CB )) or resid 85 th \ rough 87 or (resid 88 through 119 and (name N or name CA or name C or name O or \ name CB )) or resid 120 or (resid 121 through 132 and (name N or name CA or name \ C or name O or name CB )) or resid 133 or (resid 134 through 148 and (name N or \ name CA or name C or name O or name CB )) or resid 149 or (resid 150 through 15 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 158 or (resi \ d 159 and (name N or name CA or name C or name O or name CB )) or resid 160 or ( \ resid 161 through 166 and (name N or name CA or name C or name O or name CB )) o \ r resid 167 through 168 or (resid 169 through 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 or (resid 172 through 202 and (name N or \ name CA or name C or name O or name CB )) or resid 203 or (resid 204 through 22 \ 3 and (name N or name CA or name C or name O or name CB )) or (resid 224 through \ 253 and (name N or name CA or name C or name O or name CB )) or resid 254 or (r \ esid 255 and (name N or name CA or name C or name O or name CB )) or resid 256 o \ r (resid 257 through 265 and (name N or name CA or name C or name O or name CB ) \ ) or resid 266 or (resid 267 through 271 and (name N or name CA or name C or nam \ e O or name CB )) or resid 272 or (resid 273 through 276 and (name N or name CA \ or name C or name O or name CB )) or resid 277 through 278 or (resid 279 and (na \ me N or name CA or name C or name O or name CB )) or resid 280 or (resid 281 thr \ ough 290 and (name N or name CA or name C or name O or name CB )) or resid 291 t \ hrough 292 or (resid 293 through 360 and (name N or name CA or name C or name O \ or name CB )) or resid 361 or (resid 362 through 368 and (name N or name CA or n \ ame C or name O or name CB )) or resid 369 or (resid 370 through 421 and (name N \ or name CA or name C or name O or name CB )) or resid 422 or (resid 423 through \ 429 and (name N or name CA or name C or name O or name CB )) or (resid 430 thro \ ugh 453 and (name N or name CA or name C or name O or name CB )) or resid 454 or \ (resid 455 through 468 and (name N or name CA or name C or name O or name CB )) \ or resid 469 or (resid 470 through 483 and (name N or name CA or name C or name \ O or name CB )) or resid 484 or (resid 485 through 500 and (name N or name CA o \ r name C or name O or name CB )) or resid 501 or (resid 502 through 512 and (nam \ e N or name CA or name C or name O or name CB )) or resid 513 or (resid 514 thro \ ugh 554 and (name N or name CA or name C or name O or name CB )) or resid 555 or \ (resid 556 and (name N or name CA or name C or name O or name CB )) or resid 55 \ 7 or (resid 558 through 587 and (name N or name CA or name C or name O or name C \ B )) or resid 588 or (resid 589 through 591 and (name N or name CA or name C or \ name O or name CB )) or resid 592 through 593 or (resid 594 through 601 and (nam \ e N or name CA or name C or name O or name CB )) or resid 602 through 603 or (re \ sid 604 through 617 and (name N or name CA or name C or name O or name CB )) or \ resid 618 or (resid 619 through 631 and (name N or name CA or name C or name O o \ r name CB )) or resid 632 or (resid 633 through 640 and (name N or name CA or na \ me C or name O or name CB )) or resid 641 or (resid 642 through 682 and (name N \ or name CA or name C or name O or name CB )) or resid 683 or (resid 684 through \ 687 and (name N or name CA or name C or name O or name CB )) or resid 688 throug \ h 690 or (resid 691 through 705 and (name N or name CA or name C or name O or na \ me CB )) or resid 706 or (resid 707 through 712 and (name N or name CA or name C \ or name O or name CB )) or resid 713 or (resid 714 through 720 and (name N or n \ ame CA or name C or name O or name CB )) or resid 721 or (resid 722 through 726 \ and (name N or name CA or name C or name O or name CB )) or resid 727 or (resid \ 728 through 738 and (name N or name CA or name C or name O or name CB )))) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'U' and ((resid 36 through 71 and (name N or name CA or name C or name O \ or name CB )) or (resid 72 through 130 and (name N or name CA or name C or name \ O or name CB )) or resid 131 or (resid 132 through 203 and (name N or name CA or \ name C or name O or name CB )) or resid 204 or (resid 205 through 208 and (name \ N or name CA or name C or name O or name CB )) or resid 209 or (resid 210 throu \ gh 226 and (name N or name CA or name C or name O or name CB )) or resid 227 or \ (resid 228 through 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 or (resid 290 through 338 and (name N or name CA or name C or name \ O or name CB )) or resid 339 or (resid 340 through 376 and (name N or name CA or \ name C or name O or name CB )) or resid 377 or (resid 378 through 388 and (name \ N or name CA or name C or name O or name CB )) or resid 389 or (resid 390 throu \ gh 394 and (name N or name CA or name C or name O or name CB )) or resid 395 or \ (resid 396 through 401 and (name N or name CA or name C or name O or name CB )) \ or resid 402 or (resid 403 through 407 and (name N or name CA or name C or name \ O or name CB )) or resid 408 or (resid 409 through 410 and (name N or name CA or \ name C or name O or name CB )) or resid 411 or (resid 412 through 426 and (name \ N or name CA or name C or name O or name CB )) or resid 427 or (resid 428 throu \ gh 458 and (name N or name CA or name C or name O or name CB )) or resid 459 or \ (resid 460 through 467 and (name N or name CA or name C or name O or name CB )) \ or resid 468 or (resid 469 through 504 and (name N or name CA or name C or name \ O or name CB )) or (resid 505 through 562 and (name N or name CA or name C or na \ me O or name CB )) or resid 563 or (resid 564 through 565 and (name N or name CA \ or name C or name O or name CB )) or resid 566 or (resid 567 through 622 and (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'V' and ((resid 36 through 71 and (name N or name CA or name C or name O \ or name CB )) or (resid 72 through 130 and (name N or name CA or name C or name \ O or name CB )) or resid 131 or (resid 132 through 203 and (name N or name CA or \ name C or name O or name CB )) or resid 204 or (resid 205 through 208 and (name \ N or name CA or name C or name O or name CB )) or resid 209 or (resid 210 throu \ gh 226 and (name N or name CA or name C or name O or name CB )) or resid 227 or \ (resid 228 through 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 or (resid 290 through 338 and (name N or name CA or name C or name \ O or name CB )) or resid 339 or (resid 340 through 376 and (name N or name CA or \ name C or name O or name CB )) or resid 377 or (resid 378 through 388 and (name \ N or name CA or name C or name O or name CB )) or resid 389 or (resid 390 throu \ gh 394 and (name N or name CA or name C or name O or name CB )) or resid 395 or \ (resid 396 through 401 and (name N or name CA or name C or name O or name CB )) \ or resid 402 or (resid 403 through 407 and (name N or name CA or name C or name \ O or name CB )) or resid 408 or (resid 409 through 410 and (name N or name CA or \ name C or name O or name CB )) or resid 411 or (resid 412 through 426 and (name \ N or name CA or name C or name O or name CB )) or resid 427 or (resid 428 throu \ gh 458 and (name N or name CA or name C or name O or name CB )) or resid 459 or \ (resid 460 through 467 and (name N or name CA or name C or name O or name CB )) \ or resid 468 or (resid 469 through 504 and (name N or name CA or name C or name \ O or name CB )) or (resid 505 through 562 and (name N or name CA or name C or na \ me O or name CB )) or resid 563 or (resid 564 through 565 and (name N or name CA \ or name C or name O or name CB )) or resid 566 or (resid 567 through 622 and (n \ ame N or name CA or name C or name O or name CB )))) selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.660 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.090 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 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 : 0.005 0.198 34812 Z= 0.289 Angle : 0.879 32.185 47764 Z= 0.535 Chirality : 0.047 0.311 5606 Planarity : 0.005 0.192 6456 Dihedral : 16.371 89.825 11086 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.59 % Favored : 93.11 % Rotamer: Outliers : 0.66 % Allowed : 27.81 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.11), residues: 5156 helix: 0.69 (0.13), residues: 1456 sheet: -1.49 (0.18), residues: 784 loop : -1.58 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 595 TYR 0.015 0.001 TYR U 253 PHE 0.022 0.001 PHE U 529 TRP 0.052 0.001 TRP U 495 HIS 0.006 0.001 HIS V 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.29 (34796) covalent geometry : angle 0.87456 / 0.53 (47724) SS BOND : bond 0.00997 / 0.38 ( 8) SS BOND : angle 2.47567 / 1.47 ( 16) hydrogen bonds : bond 0.19612 / 12.81 ( 1338) hydrogen bonds : angle 6.85983 / 4.85 ( 3762) link_BETA1-4 : bond 0.00118 / 0.08 ( 2) link_BETA1-4 : angle 1.33645 / 0.67 ( 6) link_NAG-ASN : bond 0.01567 / 1.05 ( 6) link_NAG-ASN : angle 4.30776 / 2.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 224 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7629 (tp) REVERT: B 634 MET cc_start: 0.8113 (tpp) cc_final: 0.7885 (tpp) REVERT: U 233 MET cc_start: 0.8549 (tpp) cc_final: 0.8325 (tpp) REVERT: U 464 LEU cc_start: 0.6713 (tp) cc_final: 0.6275 (tp) outliers start: 15 outliers final: 6 residues processed: 232 average time/residue: 0.1884 time to fit residues: 73.3692 Evaluate side-chains 221 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 214 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain V residue 168 ASP Chi-restraints excluded: chain V residue 372 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 394 optimal weight: 10.0000 chunk 430 optimal weight: 40.0000 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 chunk 497 optimal weight: 50.0000 chunk 414 optimal weight: 20.0000 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 40.0000 chunk 366 optimal weight: 4.9990 chunk 223 optimal weight: 0.4980 chunk 142 optimal weight: 0.7980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS B 719 HIS U 384 GLN ** U 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 401 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.171956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.146432 restraints weight = 75815.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.144435 restraints weight = 109928.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.140496 restraints weight = 99521.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.140518 restraints weight = 96752.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.140005 restraints weight = 71734.216| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 34812 Z= 0.282 Angle : 0.663 7.968 47764 Z= 0.353 Chirality : 0.048 0.226 5606 Planarity : 0.005 0.066 6456 Dihedral : 8.266 74.945 5898 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.52 % Favored : 93.37 % Rotamer: Outliers : 4.96 % Allowed : 25.62 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.12), residues: 5156 helix: 1.56 (0.14), residues: 1508 sheet: -1.37 (0.19), residues: 744 loop : -1.29 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG U 595 TYR 0.030 0.002 TYR V 494 PHE 0.035 0.002 PHE B 331 TRP 0.023 0.002 TRP U 577 HIS 0.011 0.001 HIS V 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.28 (34796) covalent geometry : angle 0.65972 / 0.35 (47724) SS BOND : bond 0.00893 / 0.36 ( 8) SS BOND : angle 2.16372 / 1.24 ( 16) hydrogen bonds : bond 0.04589 / 3.01 ( 1338) hydrogen bonds : angle 5.16809 / 3.66 ( 3762) link_BETA1-4 : bond 0.00099 / 0.07 ( 2) link_BETA1-4 : angle 2.01543 / 1.20 ( 6) link_NAG-ASN : bond 0.00719 / 0.48 ( 6) link_NAG-ASN : angle 2.28722 / 1.46 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 223 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.8184 (t) REVERT: A 306 GLN cc_start: 0.6887 (pm20) cc_final: 0.6357 (pm20) REVERT: A 378 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8658 (tt) REVERT: A 624 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8724 (mm) REVERT: B 704 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7242 (mpp80) REVERT: U 58 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8054 (mt) REVERT: U 464 LEU cc_start: 0.6846 (tp) cc_final: 0.6551 (tp) REVERT: U 472 MET cc_start: 0.7249 (tpt) cc_final: 0.6968 (tpt) REVERT: V 116 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7848 (tm-30) REVERT: V 358 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7492 (ttm) REVERT: V 360 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7326 (mtp85) REVERT: V 568 VAL cc_start: 0.8089 (OUTLIER) cc_final: 0.7842 (p) outliers start: 113 outliers final: 62 residues processed: 320 average time/residue: 0.1835 time to fit residues: 99.5939 Evaluate side-chains 286 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 216 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 148 TRP Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 732 MET Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 214 THR Chi-restraints excluded: chain U residue 272 SER Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 358 MET Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 466 TYR Chi-restraints excluded: chain U residue 484 VAL Chi-restraints excluded: chain U residue 501 ILE Chi-restraints excluded: chain U residue 519 LEU Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 168 ASP Chi-restraints excluded: chain V residue 181 ILE Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 239 LEU Chi-restraints excluded: chain V residue 280 MET Chi-restraints excluded: chain V residue 283 CYS Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 358 MET Chi-restraints excluded: chain V residue 360 ARG Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 406 THR Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 455 VAL Chi-restraints excluded: chain V residue 488 VAL Chi-restraints excluded: chain V residue 494 TYR Chi-restraints excluded: chain V residue 568 VAL Chi-restraints excluded: chain V residue 577 TRP Chi-restraints excluded: chain V residue 587 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 202 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 415 optimal weight: 2.9990 chunk 494 optimal weight: 0.0980 chunk 221 optimal weight: 0.6980 chunk 432 optimal weight: 0.0170 chunk 416 optimal weight: 40.0000 chunk 211 optimal weight: 0.5980 chunk 352 optimal weight: 40.0000 chunk 36 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 GLN A 561 GLN A 680 ASN A 717 HIS V 148 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.174548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.152686 restraints weight = 73660.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.148118 restraints weight = 89974.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.145523 restraints weight = 87887.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.145009 restraints weight = 73191.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.143836 restraints weight = 69035.669| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 34812 Z= 0.097 Angle : 0.512 10.976 47764 Z= 0.271 Chirality : 0.043 0.190 5606 Planarity : 0.004 0.051 6456 Dihedral : 7.447 82.905 5895 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.71 % Favored : 95.17 % Rotamer: Outliers : 4.04 % Allowed : 25.79 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.12), residues: 5156 helix: 1.99 (0.14), residues: 1512 sheet: -1.22 (0.18), residues: 848 loop : -1.11 (0.12), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG V 595 TYR 0.017 0.001 TYR V 494 PHE 0.018 0.001 PHE V 529 TRP 0.030 0.001 TRP U 495 HIS 0.005 0.001 HIS A 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (34796) covalent geometry : angle 0.50996 / 0.27 (47724) SS BOND : bond 0.00700 / 0.35 ( 8) SS BOND : angle 1.75255 / 1.04 ( 16) hydrogen bonds : bond 0.03029 / 2.02 ( 1338) hydrogen bonds : angle 4.41303 / 3.13 ( 3762) link_BETA1-4 : bond 0.00339 / 0.23 ( 2) link_BETA1-4 : angle 1.37386 / 0.67 ( 6) link_NAG-ASN : bond 0.00705 / 0.48 ( 6) link_NAG-ASN : angle 1.90496 / 1.29 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 242 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6157 (tpt) REVERT: A 574 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: A 624 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8692 (mm) REVERT: A 732 MET cc_start: 0.7495 (tpp) cc_final: 0.7041 (tpp) REVERT: B 704 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7252 (mpp80) REVERT: U 179 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8784 (mp) REVERT: U 233 MET cc_start: 0.8612 (tpp) cc_final: 0.8383 (tpp) REVERT: U 464 LEU cc_start: 0.6447 (tp) cc_final: 0.6115 (tp) REVERT: U 472 MET cc_start: 0.7263 (tpt) cc_final: 0.6879 (tpt) REVERT: V 116 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7496 (tm-30) REVERT: V 291 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8728 (pt) REVERT: V 358 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.7132 (ttm) REVERT: V 464 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8398 (tt) REVERT: V 544 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7491 (mmt90) REVERT: V 568 VAL cc_start: 0.7948 (OUTLIER) cc_final: 0.7624 (p) outliers start: 92 outliers final: 38 residues processed: 317 average time/residue: 0.1880 time to fit residues: 101.4724 Evaluate side-chains 270 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 222 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 325 SER Chi-restraints excluded: chain U residue 358 MET Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 484 VAL Chi-restraints excluded: chain U residue 501 ILE Chi-restraints excluded: chain U residue 519 LEU Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 168 ASP Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 358 MET Chi-restraints excluded: chain V residue 406 THR Chi-restraints excluded: chain V residue 464 LEU Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 501 ILE Chi-restraints excluded: chain V residue 544 ARG Chi-restraints excluded: chain V residue 568 VAL Chi-restraints excluded: chain V residue 577 TRP Chi-restraints excluded: chain V residue 587 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 153 optimal weight: 0.1980 chunk 319 optimal weight: 0.9990 chunk 339 optimal weight: 50.0000 chunk 199 optimal weight: 1.9990 chunk 433 optimal weight: 50.0000 chunk 283 optimal weight: 40.0000 chunk 447 optimal weight: 7.9990 chunk 381 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 293 optimal weight: 4.9990 chunk 427 optimal weight: 40.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 ASN ** U 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.172407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.150586 restraints weight = 73215.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.146362 restraints weight = 91197.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.143217 restraints weight = 90666.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.143014 restraints weight = 79906.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.142030 restraints weight = 64863.041| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 34812 Z= 0.174 Angle : 0.550 11.511 47764 Z= 0.289 Chirality : 0.045 0.244 5606 Planarity : 0.004 0.051 6456 Dihedral : 7.361 84.913 5894 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.53 % Favored : 94.36 % Rotamer: Outliers : 4.79 % Allowed : 25.92 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.12), residues: 5156 helix: 2.06 (0.14), residues: 1508 sheet: -1.27 (0.18), residues: 880 loop : -1.17 (0.12), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 595 TYR 0.028 0.001 TYR V 494 PHE 0.026 0.001 PHE B 331 TRP 0.025 0.001 TRP U 495 HIS 0.007 0.001 HIS V 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (34796) covalent geometry : angle 0.54661 / 0.29 (47724) SS BOND : bond 0.00936 / 0.32 ( 8) SS BOND : angle 2.76757 / 1.56 ( 16) hydrogen bonds : bond 0.03264 / 2.16 ( 1338) hydrogen bonds : angle 4.31523 / 3.06 ( 3762) link_BETA1-4 : bond 0.00140 / 0.09 ( 2) link_BETA1-4 : angle 1.81912 / 1.01 ( 6) link_NAG-ASN : bond 0.00543 / 0.37 ( 6) link_NAG-ASN : angle 1.77358 / 1.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 226 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6192 (tpt) REVERT: A 624 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8743 (mm) REVERT: B 112 ASP cc_start: 0.7366 (t0) cc_final: 0.7101 (t0) REVERT: B 704 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7236 (mpp80) REVERT: U 42 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8187 (ttp80) REVERT: U 179 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8844 (mp) REVERT: U 213 ARG cc_start: 0.7922 (tpp-160) cc_final: 0.7614 (tpp-160) REVERT: U 464 LEU cc_start: 0.6534 (tp) cc_final: 0.6200 (tp) REVERT: U 472 MET cc_start: 0.7149 (tpt) cc_final: 0.6771 (tpt) REVERT: V 116 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7603 (tm-30) REVERT: V 358 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7371 (ttm) REVERT: V 365 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8042 (mt0) REVERT: V 437 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7470 (m-30) REVERT: V 464 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8423 (tt) REVERT: V 544 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7610 (mmt90) REVERT: V 568 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7574 (p) outliers start: 109 outliers final: 67 residues processed: 319 average time/residue: 0.1964 time to fit residues: 104.4618 Evaluate side-chains 294 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 216 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain U residue 42 ARG Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 325 SER Chi-restraints excluded: chain U residue 358 MET Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 484 VAL Chi-restraints excluded: chain U residue 494 TYR Chi-restraints excluded: chain U residue 501 ILE Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 168 ASP Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 239 LEU Chi-restraints excluded: chain V residue 248 ARG Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 358 MET Chi-restraints excluded: chain V residue 365 GLN Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 406 THR Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 464 LEU Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 494 TYR Chi-restraints excluded: chain V residue 501 ILE Chi-restraints excluded: chain V residue 521 VAL Chi-restraints excluded: chain V residue 544 ARG Chi-restraints excluded: chain V residue 568 VAL Chi-restraints excluded: chain V residue 587 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 152 optimal weight: 0.4980 chunk 241 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 20 optimal weight: 0.0670 chunk 390 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 486 optimal weight: 20.0000 chunk 283 optimal weight: 0.2980 chunk 314 optimal weight: 10.0000 chunk 477 optimal weight: 9.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN ** U 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.174233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.152512 restraints weight = 73585.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.147096 restraints weight = 87890.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.144546 restraints weight = 90024.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.144598 restraints weight = 74955.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.143255 restraints weight = 66979.210| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 34812 Z= 0.090 Angle : 0.490 11.776 47764 Z= 0.256 Chirality : 0.043 0.180 5606 Planarity : 0.003 0.049 6456 Dihedral : 6.893 84.509 5894 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.40 % Favored : 95.46 % Rotamer: Outliers : 4.26 % Allowed : 26.27 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.12), residues: 5156 helix: 2.19 (0.14), residues: 1508 sheet: -1.06 (0.18), residues: 872 loop : -1.08 (0.12), residues: 2776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG V 595 TYR 0.022 0.001 TYR V 494 PHE 0.019 0.001 PHE V 529 TRP 0.023 0.001 TRP U 495 HIS 0.004 0.000 HIS V 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (34796) covalent geometry : angle 0.48628 / 0.26 (47724) SS BOND : bond 0.00678 / 0.29 ( 8) SS BOND : angle 2.49268 / 1.40 ( 16) hydrogen bonds : bond 0.02543 / 1.70 ( 1338) hydrogen bonds : angle 4.06032 / 2.88 ( 3762) link_BETA1-4 : bond 0.00326 / 0.22 ( 2) link_BETA1-4 : angle 1.52604 / 0.77 ( 6) link_NAG-ASN : bond 0.00574 / 0.39 ( 6) link_NAG-ASN : angle 1.69024 / 1.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 234 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6110 (tpt) REVERT: A 417 MET cc_start: 0.7935 (tpt) cc_final: 0.7603 (tpt) REVERT: A 574 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: B 112 ASP cc_start: 0.7591 (t0) cc_final: 0.7297 (t0) REVERT: B 704 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7266 (mpp80) REVERT: U 42 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8097 (ttp80) REVERT: U 179 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8758 (mp) REVERT: U 213 ARG cc_start: 0.7900 (tpp-160) cc_final: 0.7620 (tpp-160) REVERT: U 464 LEU cc_start: 0.6632 (tp) cc_final: 0.6274 (tp) REVERT: U 472 MET cc_start: 0.7155 (tpt) cc_final: 0.6818 (tpt) REVERT: V 116 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7598 (tm-30) REVERT: V 291 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8786 (pt) REVERT: V 358 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7239 (ttm) REVERT: V 365 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7512 (tt0) REVERT: V 366 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: V 437 ASP cc_start: 0.7723 (OUTLIER) cc_final: 0.7449 (m-30) REVERT: V 544 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7628 (mmt90) REVERT: V 568 VAL cc_start: 0.7838 (OUTLIER) cc_final: 0.7551 (p) outliers start: 97 outliers final: 54 residues processed: 315 average time/residue: 0.1958 time to fit residues: 102.6549 Evaluate side-chains 291 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 225 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain U residue 42 ARG Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 325 SER Chi-restraints excluded: chain U residue 358 MET Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 478 GLU Chi-restraints excluded: chain U residue 484 VAL Chi-restraints excluded: chain U residue 501 ILE Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 168 ASP Chi-restraints excluded: chain V residue 181 ILE Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 303 ASP Chi-restraints excluded: chain V residue 358 MET Chi-restraints excluded: chain V residue 365 GLN Chi-restraints excluded: chain V residue 366 GLU Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 406 THR Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 494 TYR Chi-restraints excluded: chain V residue 501 ILE Chi-restraints excluded: chain V residue 544 ARG Chi-restraints excluded: chain V residue 568 VAL Chi-restraints excluded: chain V residue 577 TRP Chi-restraints excluded: chain V residue 587 ASP Chi-restraints excluded: chain V residue 591 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 297 optimal weight: 0.2980 chunk 260 optimal weight: 30.0000 chunk 140 optimal weight: 0.8980 chunk 448 optimal weight: 9.9990 chunk 192 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 430 optimal weight: 30.0000 chunk 394 optimal weight: 3.9990 chunk 495 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 427 ASN A 561 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.171420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.148353 restraints weight = 72583.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.143277 restraints weight = 90959.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.139481 restraints weight = 87563.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.139126 restraints weight = 84466.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.138267 restraints weight = 64574.610| |-----------------------------------------------------------------------------| r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 34812 Z= 0.197 Angle : 0.569 11.757 47764 Z= 0.296 Chirality : 0.045 0.300 5606 Planarity : 0.004 0.055 6456 Dihedral : 7.041 85.475 5894 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.99 % Favored : 93.87 % Rotamer: Outliers : 5.10 % Allowed : 26.41 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.12), residues: 5156 helix: 2.10 (0.14), residues: 1516 sheet: -1.20 (0.18), residues: 840 loop : -1.16 (0.12), residues: 2800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 595 TYR 0.027 0.002 TYR V 494 PHE 0.030 0.002 PHE B 331 TRP 0.018 0.001 TRP U 495 HIS 0.008 0.001 HIS V 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 (34796) covalent geometry : angle 0.56549 / 0.30 (47724) SS BOND : bond 0.01375 / 0.49 ( 8) SS BOND : angle 2.67060 / 1.53 ( 16) hydrogen bonds : bond 0.03361 / 2.23 ( 1338) hydrogen bonds : angle 4.15940 / 2.95 ( 3762) link_BETA1-4 : bond 0.00029 / 0.02 ( 2) link_BETA1-4 : angle 2.02962 / 1.16 ( 6) link_NAG-ASN : bond 0.00532 / 0.37 ( 6) link_NAG-ASN : angle 1.70525 / 1.13 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 226 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6216 (tpt) REVERT: A 417 MET cc_start: 0.8053 (tpt) cc_final: 0.7789 (tpt) REVERT: U 42 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8150 (ttp80) REVERT: U 179 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8848 (mp) REVERT: U 213 ARG cc_start: 0.7911 (tpp-160) cc_final: 0.7590 (tpp-160) REVERT: U 345 MET cc_start: 0.7447 (ttt) cc_final: 0.7170 (ttt) REVERT: U 464 LEU cc_start: 0.6511 (tp) cc_final: 0.6221 (tp) REVERT: U 472 MET cc_start: 0.7300 (tpt) cc_final: 0.6969 (tpt) REVERT: V 116 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7664 (tm-30) REVERT: V 365 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7710 (mt0) REVERT: V 366 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: V 437 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: V 544 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7689 (mmt90) REVERT: V 568 VAL cc_start: 0.7888 (OUTLIER) cc_final: 0.7616 (p) outliers start: 116 outliers final: 82 residues processed: 324 average time/residue: 0.2017 time to fit residues: 109.0319 Evaluate side-chains 307 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 217 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain U residue 42 ARG Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 325 SER Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 478 GLU Chi-restraints excluded: chain U residue 484 VAL Chi-restraints excluded: chain U residue 494 TYR Chi-restraints excluded: chain U residue 501 ILE Chi-restraints excluded: chain U residue 590 LYS Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 168 ASP Chi-restraints excluded: chain V residue 181 ILE Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 203 CYS Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 239 LEU Chi-restraints excluded: chain V residue 248 ARG Chi-restraints excluded: chain V residue 262 SER Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 300 THR Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 365 GLN Chi-restraints excluded: chain V residue 366 GLU Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 406 THR Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 494 TYR Chi-restraints excluded: chain V residue 521 VAL Chi-restraints excluded: chain V residue 544 ARG Chi-restraints excluded: chain V residue 568 VAL Chi-restraints excluded: chain V residue 587 ASP Chi-restraints excluded: chain V residue 591 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 56 optimal weight: 7.9990 chunk 345 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 265 optimal weight: 8.9990 chunk 466 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 313 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 427 ASN A 561 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN ** U 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 598 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.170246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.147067 restraints weight = 73091.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.141744 restraints weight = 90160.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.139406 restraints weight = 93446.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.138711 restraints weight = 90916.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.137724 restraints weight = 69301.789| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 34812 Z= 0.226 Angle : 0.586 11.530 47764 Z= 0.307 Chirality : 0.046 0.256 5606 Planarity : 0.004 0.070 6456 Dihedral : 7.055 85.272 5894 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.21 % Favored : 93.66 % Rotamer: Outliers : 5.84 % Allowed : 25.75 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.12), residues: 5156 helix: 1.98 (0.14), residues: 1512 sheet: -1.22 (0.19), residues: 796 loop : -1.22 (0.12), residues: 2848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 595 TYR 0.020 0.002 TYR B 114 PHE 0.029 0.002 PHE B 331 TRP 0.016 0.001 TRP U 495 HIS 0.008 0.001 HIS V 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 (34796) covalent geometry : angle 0.58269 / 0.31 (47724) SS BOND : bond 0.01118 / 0.41 ( 8) SS BOND : angle 2.75406 / 1.60 ( 16) hydrogen bonds : bond 0.03418 / 2.26 ( 1338) hydrogen bonds : angle 4.22734 / 3.00 ( 3762) link_BETA1-4 : bond 0.00080 / 0.05 ( 2) link_BETA1-4 : angle 2.25224 / 1.28 ( 6) link_NAG-ASN : bond 0.00576 / 0.40 ( 6) link_NAG-ASN : angle 1.79504 / 1.17 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 217 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6238 (tpt) REVERT: A 417 MET cc_start: 0.8099 (tpt) cc_final: 0.7760 (tpt) REVERT: B 300 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8833 (tt) REVERT: B 704 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7230 (mpp80) REVERT: U 42 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8202 (ttp80) REVERT: U 179 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8847 (mp) REVERT: U 213 ARG cc_start: 0.7999 (tpp-160) cc_final: 0.7619 (tpp-160) REVERT: U 464 LEU cc_start: 0.6737 (tp) cc_final: 0.6467 (tp) REVERT: V 365 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: V 366 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: V 568 VAL cc_start: 0.8013 (OUTLIER) cc_final: 0.7703 (p) outliers start: 133 outliers final: 98 residues processed: 337 average time/residue: 0.1918 time to fit residues: 108.4881 Evaluate side-chains 320 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 214 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain U residue 42 ARG Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 121 GLU Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 194 SER Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 214 THR Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 325 SER Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 466 TYR Chi-restraints excluded: chain U residue 478 GLU Chi-restraints excluded: chain U residue 501 ILE Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 168 ASP Chi-restraints excluded: chain V residue 181 ILE Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 203 CYS Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 239 LEU Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 248 ARG Chi-restraints excluded: chain V residue 262 SER Chi-restraints excluded: chain V residue 283 CYS Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 300 THR Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 365 GLN Chi-restraints excluded: chain V residue 366 GLU Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 406 THR Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 488 VAL Chi-restraints excluded: chain V residue 494 TYR Chi-restraints excluded: chain V residue 521 VAL Chi-restraints excluded: chain V residue 568 VAL Chi-restraints excluded: chain V residue 577 TRP Chi-restraints excluded: chain V residue 587 ASP Chi-restraints excluded: chain V residue 591 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 51 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 223 optimal weight: 0.4980 chunk 218 optimal weight: 0.9990 chunk 462 optimal weight: 40.0000 chunk 124 optimal weight: 2.9990 chunk 490 optimal weight: 30.0000 chunk 248 optimal weight: 4.9990 chunk 308 optimal weight: 30.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 427 ASN A 536 ASN A 561 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.171760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.149522 restraints weight = 72941.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.145461 restraints weight = 93434.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.142357 restraints weight = 84445.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.141453 restraints weight = 82999.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.140082 restraints weight = 70512.719| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34812 Z= 0.131 Angle : 0.527 11.636 47764 Z= 0.273 Chirality : 0.044 0.205 5606 Planarity : 0.004 0.062 6456 Dihedral : 6.746 84.350 5894 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.53 % Favored : 94.34 % Rotamer: Outliers : 5.01 % Allowed : 26.63 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.12), residues: 5156 helix: 2.11 (0.14), residues: 1516 sheet: -1.17 (0.18), residues: 836 loop : -1.18 (0.12), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 370 TYR 0.024 0.001 TYR U 253 PHE 0.020 0.001 PHE V 529 TRP 0.021 0.001 TRP U 495 HIS 0.006 0.001 HIS V 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (34796) covalent geometry : angle 0.52384 / 0.27 (47724) SS BOND : bond 0.00821 / 0.30 ( 8) SS BOND : angle 2.31007 / 1.33 ( 16) hydrogen bonds : bond 0.02790 / 1.85 ( 1338) hydrogen bonds : angle 4.02135 / 2.86 ( 3762) link_BETA1-4 : bond 0.00125 / 0.09 ( 2) link_BETA1-4 : angle 1.93958 / 1.04 ( 6) link_NAG-ASN : bond 0.00628 / 0.43 ( 6) link_NAG-ASN : angle 1.66201 / 1.07 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 227 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 MET cc_start: 0.8098 (tpt) cc_final: 0.7706 (tpt) REVERT: A 574 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: B 704 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7313 (mpp80) REVERT: U 42 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8181 (ttp80) REVERT: U 179 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8778 (mp) REVERT: U 213 ARG cc_start: 0.7998 (tpp-160) cc_final: 0.7573 (ttm170) REVERT: U 464 LEU cc_start: 0.6649 (tp) cc_final: 0.6373 (tp) REVERT: U 519 LEU cc_start: 0.5816 (OUTLIER) cc_final: 0.5611 (pp) REVERT: V 365 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7708 (mt0) REVERT: V 366 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: V 528 MET cc_start: 0.8164 (mmm) cc_final: 0.7734 (mmm) REVERT: V 544 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7677 (mmt90) REVERT: V 568 VAL cc_start: 0.7862 (OUTLIER) cc_final: 0.7585 (p) outliers start: 114 outliers final: 84 residues processed: 328 average time/residue: 0.1873 time to fit residues: 103.0278 Evaluate side-chains 309 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 216 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain U residue 42 ARG Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 214 THR Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 325 SER Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 478 GLU Chi-restraints excluded: chain U residue 501 ILE Chi-restraints excluded: chain U residue 519 LEU Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 168 ASP Chi-restraints excluded: chain V residue 181 ILE Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 203 CYS Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 239 LEU Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 248 ARG Chi-restraints excluded: chain V residue 262 SER Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 365 GLN Chi-restraints excluded: chain V residue 366 GLU Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 406 THR Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 494 TYR Chi-restraints excluded: chain V residue 501 ILE Chi-restraints excluded: chain V residue 521 VAL Chi-restraints excluded: chain V residue 544 ARG Chi-restraints excluded: chain V residue 568 VAL Chi-restraints excluded: chain V residue 577 TRP Chi-restraints excluded: chain V residue 587 ASP Chi-restraints excluded: chain V residue 591 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 168 optimal weight: 0.0040 chunk 384 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 238 optimal weight: 0.9980 chunk 421 optimal weight: 50.0000 chunk 345 optimal weight: 9.9990 chunk 404 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 486 optimal weight: 20.0000 chunk 299 optimal weight: 20.0000 chunk 77 optimal weight: 0.6980 overall best weight: 2.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 427 ASN A 536 ASN A 561 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 169 ASN V 486 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.170617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.147745 restraints weight = 72794.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.143193 restraints weight = 89890.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.139624 restraints weight = 87566.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.138505 restraints weight = 79712.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.137075 restraints weight = 72430.248| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 34812 Z= 0.192 Angle : 0.572 11.517 47764 Z= 0.296 Chirality : 0.045 0.279 5606 Planarity : 0.004 0.067 6456 Dihedral : 6.758 84.717 5894 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.42 % Favored : 93.44 % Rotamer: Outliers : 4.96 % Allowed : 26.93 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.12), residues: 5156 helix: 2.08 (0.14), residues: 1512 sheet: -1.22 (0.18), residues: 836 loop : -1.20 (0.12), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG V 370 TYR 0.030 0.001 TYR U 253 PHE 0.026 0.002 PHE B 331 TRP 0.019 0.001 TRP U 495 HIS 0.007 0.001 HIS V 310 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (34796) covalent geometry : angle 0.56826 / 0.29 (47724) SS BOND : bond 0.01514 / 0.49 ( 8) SS BOND : angle 2.64018 / 1.53 ( 16) hydrogen bonds : bond 0.03183 / 2.10 ( 1338) hydrogen bonds : angle 4.10062 / 2.92 ( 3762) link_BETA1-4 : bond 0.00129 / 0.09 ( 2) link_BETA1-4 : angle 2.12834 / 1.20 ( 6) link_NAG-ASN : bond 0.00547 / 0.38 ( 6) link_NAG-ASN : angle 1.69605 / 1.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 218 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6193 (tpt) REVERT: A 417 MET cc_start: 0.8113 (tpt) cc_final: 0.7731 (tpt) REVERT: B 704 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7271 (mpp80) REVERT: U 42 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8187 (ttp80) REVERT: U 179 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8825 (mp) REVERT: U 213 ARG cc_start: 0.7970 (tpp-160) cc_final: 0.7638 (tpp-160) REVERT: U 464 LEU cc_start: 0.6692 (tp) cc_final: 0.6440 (tp) REVERT: U 577 TRP cc_start: 0.7035 (p-90) cc_final: 0.6621 (p-90) REVERT: V 253 TYR cc_start: 0.7152 (t80) cc_final: 0.6840 (t80) REVERT: V 365 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7700 (mt0) REVERT: V 366 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: V 528 MET cc_start: 0.8162 (mmm) cc_final: 0.7781 (mmm) REVERT: V 544 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7695 (mmt90) REVERT: V 568 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7641 (p) outliers start: 113 outliers final: 95 residues processed: 321 average time/residue: 0.1909 time to fit residues: 102.7893 Evaluate side-chains 321 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 218 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain U residue 42 ARG Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 121 GLU Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 194 SER Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 214 THR Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 325 SER Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 466 TYR Chi-restraints excluded: chain U residue 478 GLU Chi-restraints excluded: chain U residue 501 ILE Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 168 ASP Chi-restraints excluded: chain V residue 181 ILE Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 203 CYS Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 239 LEU Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 248 ARG Chi-restraints excluded: chain V residue 262 SER Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 365 GLN Chi-restraints excluded: chain V residue 366 GLU Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 406 THR Chi-restraints excluded: chain V residue 437 ASP Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 486 ASN Chi-restraints excluded: chain V residue 494 TYR Chi-restraints excluded: chain V residue 521 VAL Chi-restraints excluded: chain V residue 544 ARG Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 568 VAL Chi-restraints excluded: chain V residue 587 ASP Chi-restraints excluded: chain V residue 591 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 439 optimal weight: 50.0000 chunk 208 optimal weight: 1.9990 chunk 423 optimal weight: 40.0000 chunk 341 optimal weight: 50.0000 chunk 366 optimal weight: 20.0000 chunk 405 optimal weight: 30.0000 chunk 475 optimal weight: 4.9990 chunk 300 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 473 optimal weight: 9.9990 chunk 362 optimal weight: 30.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 427 ASN A 536 ASN A 561 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 HIS ** U 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.170653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.147549 restraints weight = 75178.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.144546 restraints weight = 98153.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.141728 restraints weight = 88225.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.140915 restraints weight = 83363.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.139099 restraints weight = 83404.017| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.222 34812 Z= 0.651 Angle : 0.820 59.200 47764 Z= 0.468 Chirality : 0.067 0.852 5606 Planarity : 0.005 0.062 6456 Dihedral : 6.834 84.735 5894 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.57 % Favored : 93.27 % Rotamer: Outliers : 5.27 % Allowed : 26.67 % Favored : 68.06 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.12), residues: 5156 helix: 1.87 (0.14), residues: 1512 sheet: -1.23 (0.19), residues: 836 loop : -1.26 (0.12), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG V 155 TYR 0.037 0.004 TYR B 268 PHE 0.037 0.004 PHE B 331 TRP 0.018 0.003 TRP U 495 HIS 0.013 0.002 HIS V 235 Details of bonding type rmsd/Z covalent geometry : bond 0.01550 / 0.65 (34796) covalent geometry : angle 0.81664 / 0.47 (47724) SS BOND : bond 0.02413 / 0.72 ( 8) SS BOND : angle 3.15868 / 1.84 ( 16) hydrogen bonds : bond 0.04015 / 2.63 ( 1338) hydrogen bonds : angle 4.16780 / 2.96 ( 3762) link_BETA1-4 : bond 0.00923 / 0.63 ( 2) link_BETA1-4 : angle 2.81027 / 1.52 ( 6) link_NAG-ASN : bond 0.00475 / 0.33 ( 6) link_NAG-ASN : angle 1.69532 / 1.09 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 221 time to evaluate : 1.334 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 376 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6214 (tpt) REVERT: A 417 MET cc_start: 0.8149 (tpt) cc_final: 0.7820 (tpt) REVERT: U 42 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8179 (ttp80) REVERT: U 179 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8887 (mp) REVERT: U 213 ARG cc_start: 0.8034 (tpp-160) cc_final: 0.7686 (tpp-160) REVERT: U 464 LEU cc_start: 0.6697 (tp) cc_final: 0.6449 (tp) REVERT: U 577 TRP cc_start: 0.6947 (p-90) cc_final: 0.6559 (p-90) REVERT: V 253 TYR cc_start: 0.7264 (t80) cc_final: 0.6914 (t80) REVERT: V 365 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7606 (mt0) REVERT: V 366 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: V 528 MET cc_start: 0.8121 (mmm) cc_final: 0.7711 (mmm) REVERT: V 544 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7742 (mmt90) REVERT: V 568 VAL cc_start: 0.7852 (OUTLIER) cc_final: 0.7588 (p) outliers start: 120 outliers final: 102 residues processed: 331 average time/residue: 0.1934 time to fit residues: 107.1579 Evaluate side-chains 326 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 217 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 323 TYR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 ASN Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain U residue 42 ARG Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 121 GLU Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 194 SER Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 214 THR Chi-restraints excluded: chain U residue 218 ILE Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 466 TYR Chi-restraints excluded: chain U residue 478 GLU Chi-restraints excluded: chain U residue 484 VAL Chi-restraints excluded: chain U residue 501 ILE Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 168 ASP Chi-restraints excluded: chain V residue 176 THR Chi-restraints excluded: chain V residue 181 ILE Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 203 CYS Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 239 LEU Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 248 ARG Chi-restraints excluded: chain V residue 262 SER Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 365 GLN Chi-restraints excluded: chain V residue 366 GLU Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 406 THR Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 488 VAL Chi-restraints excluded: chain V residue 494 TYR Chi-restraints excluded: chain V residue 501 ILE Chi-restraints excluded: chain V residue 521 VAL Chi-restraints excluded: chain V residue 544 ARG Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 568 VAL Chi-restraints excluded: chain V residue 587 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 79 optimal weight: 0.7980 chunk 495 optimal weight: 8.9990 chunk 263 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 424 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 343 optimal weight: 50.0000 chunk 179 optimal weight: 0.8980 chunk 478 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 561 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.171483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.148001 restraints weight = 74906.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.145119 restraints weight = 96921.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.142277 restraints weight = 94044.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.142251 restraints weight = 87263.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.142024 restraints weight = 66383.341| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.171 34812 Z= 0.436 Angle : 0.955 59.200 47764 Z= 0.571 Chirality : 0.058 1.485 5606 Planarity : 0.006 0.247 6456 Dihedral : 6.836 84.675 5894 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.54 % Favored : 93.29 % Rotamer: Outliers : 4.96 % Allowed : 27.02 % Favored : 68.01 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.12), residues: 5156 helix: 1.96 (0.14), residues: 1508 sheet: -1.24 (0.18), residues: 836 loop : -1.25 (0.12), residues: 2812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 317 TYR 0.028 0.003 TYR B 268 PHE 0.039 0.003 PHE B 331 TRP 0.017 0.002 TRP U 495 HIS 0.442 0.004 HIS B 681 Details of bonding type rmsd/Z covalent geometry : bond 0.01074 / 0.44 (34796) covalent geometry : angle 0.95292 / 0.57 (47724) SS BOND : bond 0.01193 / 0.40 ( 8) SS BOND : angle 2.98477 / 1.76 ( 16) hydrogen bonds : bond 0.03535 / 2.32 ( 1338) hydrogen bonds : angle 4.15693 / 2.95 ( 3762) link_BETA1-4 : bond 0.02216 / 1.58 ( 2) link_BETA1-4 : angle 2.88646 / 1.61 ( 6) link_NAG-ASN : bond 0.00529 / 0.36 ( 6) link_NAG-ASN : angle 1.67528 / 1.07 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5802.42 seconds wall clock time: 100 minutes 37.20 seconds (6037.20 seconds total)