Starting phenix.real_space_refine on Tue Aug 26 06:09:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zgc_60075/08_2025/8zgc_60075.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zgc_60075/08_2025/8zgc_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_60075/08_2025/8zgc_60075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zgc_60075/08_2025/8zgc_60075.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zgc_60075/08_2025/8zgc_60075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zgc_60075/08_2025/8zgc_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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, 65 Unusual residues: {' MN': 1, 'AKG': 1, 'FE2': 1, 'NAG': 2, 'UDP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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, 65 Unusual residues: {' MN': 1, 'AKG': 1, 'FE2': 1, 'NAG': 2, 'UDP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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, 63 Unusual residues: {' MN': 2, 'GDU': 1, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 63 Unusual residues: {' MN': 2, 'GDU': 1, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 10.26, per 1000 atoms: 0.30 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: 3.38 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.76 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: 8.89 Time building geometry restraints manager: 4.39 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: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 37.790 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.100 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 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 aren 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 covalent geometry : bond 0.00459 (34796) covalent geometry : angle 0.87456 (47724) SS BOND : bond 0.00997 ( 8) SS BOND : angle 2.47567 ( 16) hydrogen bonds : bond 0.19612 ( 1338) hydrogen bonds : angle 6.85983 ( 3762) link_BETA1-4 : bond 0.00118 ( 2) link_BETA1-4 : angle 1.33645 ( 6) link_NAG-ASN : bond 0.01567 ( 6) link_NAG-ASN : angle 4.30776 ( 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 : 1.425 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: 0.2089 time to fit residues: 81.0253 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 : 1.710 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 719 HIS U 384 GLN U 578 ASN 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 = 0.172177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.146282 restraints weight = 75360.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.144305 restraints weight = 113893.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.141095 restraints weight = 95602.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.141114 restraints weight = 90566.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.140394 restraints weight = 75096.783| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 34812 Z= 0.285 Angle : 0.662 7.997 47764 Z= 0.354 Chirality : 0.048 0.229 5606 Planarity : 0.005 0.066 6456 Dihedral : 8.255 76.154 5898 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.48 % Favored : 93.41 % Rotamer: Outliers : 4.79 % Allowed : 25.75 % 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 aren not related in a simple way. whole: -0.67 (0.12), residues: 5156 helix: 1.54 (0.14), residues: 1508 sheet: -1.43 (0.19), residues: 752 loop : -1.29 (0.11), residues: 2896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG U 595 TYR 0.031 0.002 TYR V 494 PHE 0.036 0.002 PHE B 331 TRP 0.022 0.002 TRP U 495 HIS 0.010 0.001 HIS V 310 Details of bonding type rmsd covalent geometry : bond 0.00682 (34796) covalent geometry : angle 0.65922 (47724) SS BOND : bond 0.00924 ( 8) SS BOND : angle 2.18966 ( 16) hydrogen bonds : bond 0.04623 ( 1338) hydrogen bonds : angle 5.15570 ( 3762) link_BETA1-4 : bond 0.00112 ( 2) link_BETA1-4 : angle 2.00146 ( 6) link_NAG-ASN : bond 0.00745 ( 6) link_NAG-ASN : angle 2.30786 ( 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 332 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 223 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8169 (t) REVERT: A 306 GLN cc_start: 0.6883 (pm20) cc_final: 0.6378 (pm20) REVERT: A 378 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8670 (tt) REVERT: A 417 MET cc_start: 0.7972 (tpt) cc_final: 0.7770 (tpt) REVERT: A 624 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8733 (mm) REVERT: B 704 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7249 (mpp80) REVERT: U 58 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8103 (mt) REVERT: U 464 LEU cc_start: 0.6830 (tp) cc_final: 0.6538 (tp) REVERT: U 472 MET cc_start: 0.7243 (tpt) cc_final: 0.6958 (tpt) REVERT: V 116 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7836 (tm-30) REVERT: V 358 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7493 (ttm) REVERT: V 360 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7337 (mtp85) REVERT: V 568 VAL cc_start: 0.8133 (OUTLIER) cc_final: 0.7903 (p) outliers start: 109 outliers final: 61 residues processed: 315 average time/residue: 0.2042 time to fit residues: 108.7813 Evaluate side-chains 285 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 216 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 497 PHE 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 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 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: 0.9990 chunk 100 optimal weight: 1.9990 chunk 415 optimal weight: 0.7980 chunk 494 optimal weight: 5.9990 chunk 221 optimal weight: 0.8980 chunk 432 optimal weight: 0.0050 chunk 416 optimal weight: 40.0000 chunk 211 optimal weight: 0.5980 chunk 352 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 GLN A 680 ASN A 717 HIS V 148 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.174111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.152300 restraints weight = 73546.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.147421 restraints weight = 87907.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.144398 restraints weight = 92286.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.144170 restraints weight = 86149.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.143397 restraints weight = 67064.046| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 34812 Z= 0.102 Angle : 0.516 11.331 47764 Z= 0.273 Chirality : 0.043 0.186 5606 Planarity : 0.004 0.051 6456 Dihedral : 7.526 76.517 5895 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.77 % Favored : 95.11 % Rotamer: Outliers : 4.22 % Allowed : 25.88 % Favored : 69.90 % 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 aren not related in a simple way. whole: -0.33 (0.12), residues: 5156 helix: 1.94 (0.14), residues: 1512 sheet: -1.22 (0.18), residues: 848 loop : -1.13 (0.12), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG U 595 TYR 0.021 0.001 TYR V 494 PHE 0.019 0.001 PHE V 529 TRP 0.029 0.001 TRP U 495 HIS 0.005 0.001 HIS A 177 Details of bonding type rmsd covalent geometry : bond 0.00224 (34796) covalent geometry : angle 0.51379 (47724) SS BOND : bond 0.00623 ( 8) SS BOND : angle 1.81802 ( 16) hydrogen bonds : bond 0.03128 ( 1338) hydrogen bonds : angle 4.44187 ( 3762) link_BETA1-4 : bond 0.00416 ( 2) link_BETA1-4 : angle 1.46560 ( 6) link_NAG-ASN : bond 0.00683 ( 6) link_NAG-ASN : angle 1.92954 ( 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 338 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 242 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 MET cc_start: 0.8031 (tpt) cc_final: 0.7673 (tpt) REVERT: A 624 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8692 (mm) REVERT: A 732 MET cc_start: 0.7544 (tpp) cc_final: 0.7101 (tpp) REVERT: B 112 ASP cc_start: 0.7654 (t0) cc_final: 0.7342 (t0) REVERT: B 704 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7254 (mpp80) REVERT: U 179 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8808 (mp) REVERT: U 233 MET cc_start: 0.8628 (tpp) cc_final: 0.8426 (tpp) REVERT: U 464 LEU cc_start: 0.6450 (tp) cc_final: 0.6187 (tp) REVERT: U 472 MET cc_start: 0.7262 (tpt) cc_final: 0.6900 (tpt) REVERT: V 116 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7554 (tm-30) REVERT: V 291 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8650 (pt) REVERT: V 358 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7184 (ttm) REVERT: V 464 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8407 (tt) REVERT: V 544 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7474 (mmt90) REVERT: V 568 VAL cc_start: 0.7971 (OUTLIER) cc_final: 0.7641 (p) outliers start: 96 outliers final: 45 residues processed: 321 average time/residue: 0.1936 time to fit residues: 105.6093 Evaluate side-chains 277 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 224 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 159 THR 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 424 LEU Chi-restraints excluded: chain A residue 458 VAL 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 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 279 CYS 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 160 ASP Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 317 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 311 VAL 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: 3.9990 chunk 319 optimal weight: 50.0000 chunk 339 optimal weight: 50.0000 chunk 199 optimal weight: 2.9990 chunk 433 optimal weight: 50.0000 chunk 283 optimal weight: 40.0000 chunk 447 optimal weight: 10.0000 chunk 381 optimal weight: 8.9990 chunk 172 optimal weight: 0.9990 chunk 293 optimal weight: 20.0000 chunk 427 optimal weight: 50.0000 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN A 561 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 HIS A 680 ASN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN ** U 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 HIS V 169 ASN V 486 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.170718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.147091 restraints weight = 74707.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.144225 restraints weight = 107117.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.141148 restraints weight = 101232.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.140474 restraints weight = 94167.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.139414 restraints weight = 83136.454| |-----------------------------------------------------------------------------| r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.140 34812 Z= 0.448 Angle : 0.792 10.842 47764 Z= 0.415 Chirality : 0.053 0.332 5606 Planarity : 0.006 0.084 6456 Dihedral : 8.167 83.867 5894 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.68 % Favored : 92.16 % Rotamer: Outliers : 7.03 % Allowed : 25.26 % Favored : 67.71 % 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 aren not related in a simple way. whole: -0.86 (0.12), residues: 5156 helix: 1.45 (0.14), residues: 1512 sheet: -1.42 (0.20), residues: 724 loop : -1.50 (0.11), residues: 2920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG V 595 TYR 0.043 0.003 TYR V 494 PHE 0.047 0.003 PHE B 331 TRP 0.020 0.002 TRP V 117 HIS 0.014 0.002 HIS V 235 Details of bonding type rmsd covalent geometry : bond 0.01073 (34796) covalent geometry : angle 0.78855 (47724) SS BOND : bond 0.01944 ( 8) SS BOND : angle 3.46415 ( 16) hydrogen bonds : bond 0.05034 ( 1338) hydrogen bonds : angle 4.95210 ( 3762) link_BETA1-4 : bond 0.00086 ( 2) link_BETA1-4 : angle 2.55647 ( 6) link_NAG-ASN : bond 0.00715 ( 6) link_NAG-ASN : angle 2.23532 ( 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 377 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 217 time to evaluate : 1.154 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 417 MET cc_start: 0.7985 (tpt) cc_final: 0.7674 (tpt) REVERT: A 624 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8771 (mm) REVERT: B 300 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8770 (tt) REVERT: U 213 ARG cc_start: 0.7979 (tpp-160) cc_final: 0.7578 (tpp-160) REVERT: U 472 MET cc_start: 0.7165 (tpt) cc_final: 0.6834 (tpt) REVERT: V 253 TYR cc_start: 0.7374 (t80) cc_final: 0.7119 (t80) REVERT: V 360 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7332 (mtp85) REVERT: V 365 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8086 (mt0) REVERT: V 464 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8421 (tt) outliers start: 160 outliers final: 118 residues processed: 362 average time/residue: 0.2061 time to fit residues: 125.2625 Evaluate side-chains 332 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 209 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 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 403 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 470 ASP 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 624 LEU Chi-restraints excluded: chain A residue 638 LEU 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 108 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 308 THR 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 398 THR Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 458 VAL 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 651 ASN Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 700 ILE Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 37 TYR 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 193 ASP Chi-restraints excluded: chain U residue 194 SER Chi-restraints excluded: chain U residue 214 THR Chi-restraints excluded: chain U residue 267 ILE Chi-restraints excluded: chain U residue 272 SER 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 358 MET Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 425 ASP Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 466 TYR Chi-restraints excluded: chain U residue 494 TYR Chi-restraints excluded: chain U residue 501 ILE Chi-restraints excluded: chain U residue 547 HIS Chi-restraints excluded: chain U residue 590 LYS Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 70 THR 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 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 280 MET 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 360 ARG 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 455 VAL Chi-restraints excluded: chain V residue 464 LEU Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 486 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 152 optimal weight: 0.8980 chunk 241 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 390 optimal weight: 0.9980 chunk 112 optimal weight: 0.6980 chunk 486 optimal weight: 20.0000 chunk 283 optimal weight: 40.0000 chunk 314 optimal weight: 0.4980 chunk 477 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN A 561 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 ASN B 561 GLN U 578 ASN U 598 GLN V 486 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.172305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.149206 restraints weight = 73232.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.144510 restraints weight = 90138.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.140369 restraints weight = 89567.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.139560 restraints weight = 83791.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.138313 restraints weight = 70915.937| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 34812 Z= 0.112 Angle : 0.536 11.188 47764 Z= 0.282 Chirality : 0.044 0.169 5606 Planarity : 0.004 0.060 6456 Dihedral : 7.373 81.819 5894 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.93 % Favored : 94.94 % Rotamer: Outliers : 4.39 % Allowed : 27.94 % Favored : 67.66 % 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 aren not related in a simple way. whole: -0.45 (0.12), residues: 5156 helix: 1.88 (0.14), residues: 1512 sheet: -1.25 (0.18), residues: 804 loop : -1.25 (0.12), residues: 2840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG V 595 TYR 0.022 0.001 TYR U 253 PHE 0.019 0.001 PHE V 529 TRP 0.022 0.001 TRP U 495 HIS 0.006 0.001 HIS V 310 Details of bonding type rmsd covalent geometry : bond 0.00252 (34796) covalent geometry : angle 0.53319 (47724) SS BOND : bond 0.00704 ( 8) SS BOND : angle 2.27236 ( 16) hydrogen bonds : bond 0.02985 ( 1338) hydrogen bonds : angle 4.31054 ( 3762) link_BETA1-4 : bond 0.00198 ( 2) link_BETA1-4 : angle 1.78836 ( 6) link_NAG-ASN : bond 0.00633 ( 6) link_NAG-ASN : angle 1.88220 ( 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 320 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 220 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 MET cc_start: 0.8177 (tpt) cc_final: 0.7619 (tpt) REVERT: A 574 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: A 624 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8718 (mm) REVERT: B 112 ASP cc_start: 0.7810 (t0) cc_final: 0.7530 (t0) REVERT: B 704 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7349 (mpp80) REVERT: U 42 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8174 (ttp80) REVERT: U 213 ARG cc_start: 0.7990 (tpp-160) cc_final: 0.7679 (tpp-160) REVERT: U 464 LEU cc_start: 0.6604 (tp) cc_final: 0.6250 (tp) REVERT: U 472 MET cc_start: 0.7363 (tpt) cc_final: 0.7044 (tpt) REVERT: V 226 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8478 (mtp85) REVERT: V 365 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7811 (mt0) REVERT: V 366 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: V 464 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8351 (tt) REVERT: V 544 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7535 (mmt90) REVERT: V 568 VAL cc_start: 0.7970 (OUTLIER) cc_final: 0.7633 (p) outliers start: 100 outliers final: 59 residues processed: 306 average time/residue: 0.1901 time to fit residues: 97.0231 Evaluate side-chains 283 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 214 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 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 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 551 ARG Chi-restraints excluded: chain A residue 574 GLU 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 724 THR Chi-restraints excluded: chain B residue 68 THR 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 285 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 458 VAL 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 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 681 HIS 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 160 ASP Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 203 CYS 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 358 MET Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 494 TYR Chi-restraints excluded: chain U residue 501 ILE 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 214 THR Chi-restraints excluded: chain V residue 226 ARG 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 464 LEU Chi-restraints excluded: chain V residue 474 VAL 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 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: 1.9990 chunk 260 optimal weight: 50.0000 chunk 140 optimal weight: 0.9990 chunk 448 optimal weight: 8.9990 chunk 192 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 430 optimal weight: 30.0000 chunk 394 optimal weight: 50.0000 chunk 495 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 = 0.4476 r_free = 0.4476 target = 0.172413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.146812 restraints weight = 74637.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.144771 restraints weight = 113711.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.141010 restraints weight = 100401.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.140932 restraints weight = 98722.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.140447 restraints weight = 75495.178| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 34812 Z= 0.262 Angle : 0.624 11.156 47764 Z= 0.327 Chirality : 0.047 0.296 5606 Planarity : 0.005 0.065 6456 Dihedral : 7.437 82.659 5894 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.00 % Favored : 92.84 % Rotamer: Outliers : 5.80 % Allowed : 26.93 % Favored : 67.27 % 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 aren not related in a simple way. whole: -0.62 (0.12), residues: 5156 helix: 1.68 (0.14), residues: 1536 sheet: -1.26 (0.20), residues: 732 loop : -1.40 (0.11), residues: 2888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG V 595 TYR 0.028 0.002 TYR V 494 PHE 0.034 0.002 PHE B 331 TRP 0.015 0.001 TRP U 495 HIS 0.009 0.001 HIS V 310 Details of bonding type rmsd covalent geometry : bond 0.00629 (34796) covalent geometry : angle 0.62027 (47724) SS BOND : bond 0.01153 ( 8) SS BOND : angle 3.10252 ( 16) hydrogen bonds : bond 0.03772 ( 1338) hydrogen bonds : angle 4.45051 ( 3762) link_BETA1-4 : bond 0.00109 ( 2) link_BETA1-4 : angle 2.27598 ( 6) link_NAG-ASN : bond 0.00593 ( 6) link_NAG-ASN : angle 1.92144 ( 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 348 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 216 time to evaluate : 1.062 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: 0.6998 (OUTLIER) cc_final: 0.6033 (tpt) REVERT: A 417 MET cc_start: 0.8071 (tpt) cc_final: 0.7584 (tpt) REVERT: A 624 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8713 (mm) REVERT: U 42 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8125 (ttp80) REVERT: U 58 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8075 (mt) REVERT: U 213 ARG cc_start: 0.7984 (tpp-160) cc_final: 0.7621 (tpp-160) REVERT: U 345 MET cc_start: 0.7478 (ttt) cc_final: 0.7180 (ttt) REVERT: U 464 LEU cc_start: 0.6721 (tp) cc_final: 0.6434 (tp) REVERT: U 472 MET cc_start: 0.7130 (tpt) cc_final: 0.6781 (tpt) REVERT: U 518 MET cc_start: 0.5156 (tpt) cc_final: 0.4645 (tpt) REVERT: V 226 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8671 (mtp85) REVERT: V 253 TYR cc_start: 0.7216 (t80) cc_final: 0.6907 (t80) REVERT: V 365 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7735 (mt0) REVERT: V 366 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: V 464 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8420 (tt) REVERT: V 487 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8904 (mt) REVERT: V 568 VAL cc_start: 0.7886 (OUTLIER) cc_final: 0.7597 (p) outliers start: 132 outliers final: 93 residues processed: 331 average time/residue: 0.1908 time to fit residues: 105.2000 Evaluate side-chains 317 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 214 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 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 445 VAL Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 476 LEU 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 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 116 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 458 VAL 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 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 58 LEU 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 193 ASP Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 205 MET Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 272 SER 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 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 U residue 517 LYS 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 203 CYS Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 226 ARG 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 464 LEU Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 487 LEU Chi-restraints excluded: chain V residue 494 TYR Chi-restraints excluded: chain V residue 521 VAL Chi-restraints excluded: chain V residue 546 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 56 optimal weight: 9.9990 chunk 345 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 265 optimal weight: 20.0000 chunk 466 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 313 optimal weight: 30.0000 chunk 244 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN A 561 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 401 HIS ** 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 = 0.4479 r_free = 0.4479 target = 0.172326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.146190 restraints weight = 75181.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.144489 restraints weight = 106709.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.141024 restraints weight = 90149.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.140953 restraints weight = 90336.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.140092 restraints weight = 75226.515| |-----------------------------------------------------------------------------| r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.2057 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= 0.194 Angle : 0.569 11.242 47764 Z= 0.299 Chirality : 0.045 0.254 5606 Planarity : 0.004 0.064 6456 Dihedral : 7.248 82.245 5894 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.76 % Favored : 94.08 % Rotamer: Outliers : 5.98 % Allowed : 26.85 % Favored : 67.18 % 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 aren not related in a simple way. whole: -0.55 (0.12), residues: 5156 helix: 1.77 (0.14), residues: 1536 sheet: -1.25 (0.20), residues: 704 loop : -1.37 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 595 TYR 0.025 0.001 TYR U 253 PHE 0.025 0.002 PHE B 331 TRP 0.017 0.001 TRP U 495 HIS 0.008 0.001 HIS V 310 Details of bonding type rmsd covalent geometry : bond 0.00463 (34796) covalent geometry : angle 0.56575 (47724) SS BOND : bond 0.01100 ( 8) SS BOND : angle 2.80465 ( 16) hydrogen bonds : bond 0.03291 ( 1338) hydrogen bonds : angle 4.29668 ( 3762) link_BETA1-4 : bond 0.00082 ( 2) link_BETA1-4 : angle 2.16998 ( 6) link_NAG-ASN : bond 0.00571 ( 6) link_NAG-ASN : angle 1.84392 ( 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 353 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 217 time to evaluate : 1.140 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: 0.7002 (OUTLIER) cc_final: 0.5997 (tpt) REVERT: A 417 MET cc_start: 0.8134 (tpt) cc_final: 0.7549 (tpt) REVERT: A 574 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: B 614 MET cc_start: 0.8455 (mmm) cc_final: 0.8148 (mmt) REVERT: U 42 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8149 (ttp80) REVERT: U 213 ARG cc_start: 0.7987 (tpp-160) cc_final: 0.7647 (tpp-160) REVERT: U 233 MET cc_start: 0.8758 (tpp) cc_final: 0.8532 (tpp) REVERT: U 464 LEU cc_start: 0.6787 (tp) cc_final: 0.6483 (tp) REVERT: V 253 TYR cc_start: 0.7170 (t80) cc_final: 0.6847 (t80) REVERT: V 365 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7718 (mt0) REVERT: V 366 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: V 464 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8394 (tt) REVERT: V 544 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7686 (mmt90) REVERT: V 568 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7630 (p) outliers start: 136 outliers final: 96 residues processed: 338 average time/residue: 0.1879 time to fit residues: 106.7498 Evaluate side-chains 317 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 213 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 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 323 TYR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 445 VAL 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 574 GLU 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 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 175 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 458 VAL 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 681 HIS 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 90 THR 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 193 ASP Chi-restraints excluded: chain U residue 203 CYS 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 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 U residue 517 LYS Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 69 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 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 311 VAL 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 464 LEU Chi-restraints excluded: chain V residue 474 VAL 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 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: 9.9990 chunk 246 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 223 optimal weight: 0.5980 chunk 218 optimal weight: 0.6980 chunk 462 optimal weight: 40.0000 chunk 124 optimal weight: 2.9990 chunk 490 optimal weight: 0.0470 chunk 248 optimal weight: 5.9990 chunk 308 optimal weight: 9.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 ASN A 536 ASN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 347 ASN ** 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 = 0.4506 r_free = 0.4506 target = 0.171997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.149515 restraints weight = 72951.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.144503 restraints weight = 86335.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.141417 restraints weight = 91300.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.140782 restraints weight = 83350.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.139642 restraints weight = 70532.034| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 34812 Z= 0.107 Angle : 0.521 11.424 47764 Z= 0.270 Chirality : 0.043 0.240 5606 Planarity : 0.004 0.054 6456 Dihedral : 6.877 82.162 5894 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.14 % Favored : 94.72 % Rotamer: Outliers : 4.66 % Allowed : 28.30 % Favored : 67.05 % 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 aren not related in a simple way. whole: -0.35 (0.12), residues: 5156 helix: 2.00 (0.14), residues: 1520 sheet: -1.17 (0.19), residues: 788 loop : -1.25 (0.12), residues: 2848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 370 TYR 0.018 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 covalent geometry : bond 0.00249 (34796) covalent geometry : angle 0.51817 (47724) SS BOND : bond 0.00757 ( 8) SS BOND : angle 2.29317 ( 16) hydrogen bonds : bond 0.02675 ( 1338) hydrogen bonds : angle 4.05849 ( 3762) link_BETA1-4 : bond 0.00305 ( 2) link_BETA1-4 : angle 1.84925 ( 6) link_NAG-ASN : bond 0.00563 ( 6) link_NAG-ASN : angle 1.70485 ( 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 333 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 227 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: 0.7083 (OUTLIER) cc_final: 0.6060 (tpt) REVERT: A 417 MET cc_start: 0.8188 (tpt) cc_final: 0.7578 (tpt) REVERT: B 112 ASP cc_start: 0.7847 (t0) cc_final: 0.7600 (t0) REVERT: B 704 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7386 (mpp80) REVERT: U 42 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8184 (ttp80) REVERT: U 213 ARG cc_start: 0.7929 (tpp-160) cc_final: 0.7650 (tpp-160) REVERT: U 464 LEU cc_start: 0.6559 (tp) cc_final: 0.6226 (tp) REVERT: U 518 MET cc_start: 0.4956 (tpt) cc_final: 0.4557 (tpt) REVERT: V 253 TYR cc_start: 0.6968 (t80) cc_final: 0.6615 (t80) REVERT: V 365 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7398 (tt0) REVERT: V 366 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: V 464 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8406 (tt) REVERT: V 544 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7661 (mmt90) REVERT: V 568 VAL cc_start: 0.7848 (OUTLIER) cc_final: 0.7599 (p) REVERT: V 594 MET cc_start: 0.6550 (mmm) cc_final: 0.6163 (mmm) outliers start: 106 outliers final: 75 residues processed: 320 average time/residue: 0.1950 time to fit residues: 104.1841 Evaluate side-chains 301 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 218 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 117 ILE 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 323 TYR 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 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 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 68 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 471 THR 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 U residue 42 ARG Chi-restraints excluded: chain U residue 47 SER 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 193 ASP Chi-restraints excluded: chain U residue 203 CYS 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 484 VAL Chi-restraints excluded: chain U residue 494 TYR Chi-restraints excluded: chain U residue 501 ILE Chi-restraints excluded: chain U residue 517 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 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 248 ARG Chi-restraints excluded: chain V residue 311 VAL 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 464 LEU Chi-restraints excluded: chain V residue 474 VAL 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 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: 0.0980 chunk 384 optimal weight: 7.9990 chunk 248 optimal weight: 8.9990 chunk 238 optimal weight: 0.0980 chunk 421 optimal weight: 9.9990 chunk 345 optimal weight: 20.0000 chunk 404 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 486 optimal weight: 20.0000 chunk 299 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 GLN A 427 ASN A 536 ASN A 561 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 169 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.171272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.145121 restraints weight = 74780.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.143309 restraints weight = 114944.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.140031 restraints weight = 98604.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.140170 restraints weight = 90931.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.140257 restraints weight = 67218.016| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.118 34812 Z= 0.328 Angle : 0.696 11.128 47764 Z= 0.363 Chirality : 0.049 0.330 5606 Planarity : 0.005 0.069 6456 Dihedral : 7.354 83.417 5894 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.87 % Favored : 91.99 % Rotamer: Outliers : 5.58 % Allowed : 27.46 % Favored : 66.96 % 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 aren not related in a simple way. whole: -0.66 (0.12), residues: 5156 helix: 1.73 (0.14), residues: 1508 sheet: -1.30 (0.20), residues: 720 loop : -1.44 (0.11), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG V 595 TYR 0.027 0.002 TYR B 460 PHE 0.042 0.002 PHE B 331 TRP 0.016 0.002 TRP V 117 HIS 0.010 0.001 HIS V 235 Details of bonding type rmsd covalent geometry : bond 0.00790 (34796) covalent geometry : angle 0.69297 (47724) SS BOND : bond 0.01353 ( 8) SS BOND : angle 2.96442 ( 16) hydrogen bonds : bond 0.04180 ( 1338) hydrogen bonds : angle 4.48788 ( 3762) link_BETA1-4 : bond 0.00519 ( 2) link_BETA1-4 : angle 2.73330 ( 6) link_NAG-ASN : bond 0.00635 ( 6) link_NAG-ASN : angle 1.88507 ( 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 343 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 216 time to evaluate : 1.342 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 73 GLU cc_start: 0.5154 (OUTLIER) cc_final: 0.4045 (mt-10) REVERT: A 376 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6048 (tpt) REVERT: A 417 MET cc_start: 0.8043 (tpt) cc_final: 0.7458 (tpt) REVERT: A 427 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8354 (p0) REVERT: B 112 ASP cc_start: 0.7918 (t0) cc_final: 0.7650 (t0) REVERT: B 300 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8806 (tt) REVERT: B 614 MET cc_start: 0.8462 (mmm) cc_final: 0.8132 (mmt) REVERT: U 42 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8108 (ttp80) REVERT: U 213 ARG cc_start: 0.8038 (tpp-160) cc_final: 0.7651 (tpp-160) REVERT: U 464 LEU cc_start: 0.6743 (tp) cc_final: 0.6461 (tp) REVERT: U 518 MET cc_start: 0.5332 (tpt) cc_final: 0.5098 (tpt) REVERT: V 41 GLU cc_start: 0.8081 (pt0) cc_final: 0.7849 (tt0) REVERT: V 253 TYR cc_start: 0.7293 (t80) cc_final: 0.6967 (t80) REVERT: V 345 MET cc_start: 0.7818 (tpt) cc_final: 0.7429 (tpt) REVERT: V 365 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7631 (mt0) REVERT: V 366 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7861 (mp0) REVERT: V 464 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8386 (tt) REVERT: V 487 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8898 (mt) REVERT: V 528 MET cc_start: 0.8139 (mmm) cc_final: 0.7766 (mmm) REVERT: V 544 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7730 (mmt90) REVERT: V 568 VAL cc_start: 0.7919 (OUTLIER) cc_final: 0.7641 (p) outliers start: 127 outliers final: 103 residues processed: 333 average time/residue: 0.2112 time to fit residues: 116.8722 Evaluate side-chains 328 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 214 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 73 GLU Chi-restraints excluded: chain A residue 117 ILE 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 323 TYR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 427 ASN Chi-restraints excluded: chain A residue 445 VAL 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 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 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 175 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 542 GLU 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 47 SER Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 177 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 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 494 TYR Chi-restraints excluded: chain U residue 501 ILE Chi-restraints excluded: chain U residue 517 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 241 ASP 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 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 410 LEU Chi-restraints excluded: chain V residue 464 LEU Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 487 LEU 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 559 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 439 optimal weight: 50.0000 chunk 208 optimal weight: 0.7980 chunk 423 optimal weight: 40.0000 chunk 341 optimal weight: 0.0030 chunk 366 optimal weight: 20.0000 chunk 405 optimal weight: 20.0000 chunk 475 optimal weight: 1.9990 chunk 300 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 473 optimal weight: 8.9990 chunk 362 optimal weight: 8.9990 overall best weight: 2.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 347 ASN ** 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 = 0.4466 r_free = 0.4466 target = 0.171525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.146606 restraints weight = 74965.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.144203 restraints weight = 114306.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.141289 restraints weight = 101570.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.141362 restraints weight = 93143.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.141316 restraints weight = 68914.567| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 34812 Z= 0.285 Angle : 0.802 59.200 47764 Z= 0.447 Chirality : 0.048 0.622 5606 Planarity : 0.005 0.130 6456 Dihedral : 7.323 83.405 5892 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.74 % Favored : 92.11 % Rotamer: Outliers : 5.05 % Allowed : 27.77 % Favored : 67.18 % Cbeta Deviations : 0.04 % 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 aren not related in a simple way. whole: -0.69 (0.12), residues: 5156 helix: 1.72 (0.14), residues: 1508 sheet: -1.34 (0.20), residues: 724 loop : -1.45 (0.11), residues: 2924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 595 TYR 0.028 0.002 TYR V 494 PHE 0.040 0.002 PHE B 331 TRP 0.015 0.001 TRP V 117 HIS 0.010 0.001 HIS V 310 Details of bonding type rmsd covalent geometry : bond 0.00681 (34796) covalent geometry : angle 0.79894 (47724) SS BOND : bond 0.01128 ( 8) SS BOND : angle 2.86236 ( 16) hydrogen bonds : bond 0.04068 ( 1338) hydrogen bonds : angle 4.47983 ( 3762) link_BETA1-4 : bond 0.01462 ( 2) link_BETA1-4 : angle 2.87280 ( 6) link_NAG-ASN : bond 0.00653 ( 6) link_NAG-ASN : angle 1.90986 ( 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 327 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 212 time to evaluate : 1.435 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 73 GLU cc_start: 0.5219 (OUTLIER) cc_final: 0.4100 (mt-10) REVERT: A 376 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6027 (tpt) REVERT: A 417 MET cc_start: 0.8043 (tpt) cc_final: 0.7474 (tpt) REVERT: B 112 ASP cc_start: 0.7893 (t0) cc_final: 0.7611 (t0) REVERT: B 300 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8792 (tt) REVERT: B 614 MET cc_start: 0.8447 (mmm) cc_final: 0.8093 (mmt) REVERT: U 42 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8127 (ttp80) REVERT: U 213 ARG cc_start: 0.8017 (tpp-160) cc_final: 0.7634 (tpp-160) REVERT: U 464 LEU cc_start: 0.6715 (tp) cc_final: 0.6434 (tp) REVERT: V 41 GLU cc_start: 0.8059 (pt0) cc_final: 0.7833 (tt0) REVERT: V 253 TYR cc_start: 0.7296 (t80) cc_final: 0.6966 (t80) REVERT: V 345 MET cc_start: 0.7807 (tpt) cc_final: 0.7406 (tpt) REVERT: V 365 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: V 366 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: V 464 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8379 (tt) REVERT: V 487 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8892 (mt) REVERT: V 528 MET cc_start: 0.8117 (mmm) cc_final: 0.7726 (mmm) REVERT: V 544 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7733 (mmt90) REVERT: V 568 VAL cc_start: 0.7910 (OUTLIER) cc_final: 0.7630 (p) outliers start: 115 outliers final: 102 residues processed: 320 average time/residue: 0.2120 time to fit residues: 112.7890 Evaluate side-chains 324 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 212 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 73 GLU Chi-restraints excluded: chain A residue 117 ILE 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 323 TYR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 445 VAL 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 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 175 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 300 LEU 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 400 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 471 THR 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 613 HIS 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 47 SER Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 177 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 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 494 TYR Chi-restraints excluded: chain U residue 501 ILE Chi-restraints excluded: chain U residue 517 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 241 ASP 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 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 410 LEU Chi-restraints excluded: chain V residue 464 LEU Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 487 LEU 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 559 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 79 optimal weight: 0.9980 chunk 495 optimal weight: 8.9990 chunk 263 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 424 optimal weight: 30.0000 chunk 177 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 343 optimal weight: 40.0000 chunk 179 optimal weight: 6.9990 chunk 478 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 347 ASN ** 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 = 0.4465 r_free = 0.4465 target = 0.171476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.145987 restraints weight = 74623.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.144134 restraints weight = 115140.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.140846 restraints weight = 102498.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.141003 restraints weight = 93410.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.141093 restraints weight = 70435.659| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 34812 Z= 0.285 Angle : 0.802 59.200 47764 Z= 0.447 Chirality : 0.048 0.622 5606 Planarity : 0.005 0.130 6456 Dihedral : 7.323 83.405 5892 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.74 % Favored : 92.11 % Rotamer: Outliers : 4.92 % Allowed : 27.99 % Favored : 67.09 % Cbeta Deviations : 0.04 % 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 aren not related in a simple way. whole: -0.69 (0.12), residues: 5156 helix: 1.72 (0.14), residues: 1508 sheet: -1.34 (0.20), residues: 724 loop : -1.45 (0.11), residues: 2924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG V 595 TYR 0.028 0.002 TYR V 494 PHE 0.040 0.002 PHE B 331 TRP 0.015 0.001 TRP V 117 HIS 0.010 0.001 HIS V 310 Details of bonding type rmsd covalent geometry : bond 0.00681 (34796) covalent geometry : angle 0.79893 (47724) SS BOND : bond 0.01128 ( 8) SS BOND : angle 2.86236 ( 16) hydrogen bonds : bond 0.04068 ( 1338) hydrogen bonds : angle 4.47983 ( 3762) link_BETA1-4 : bond 0.01462 ( 2) link_BETA1-4 : angle 2.87280 ( 6) link_NAG-ASN : bond 0.00653 ( 6) link_NAG-ASN : angle 1.90986 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5674.34 seconds wall clock time: 98 minutes 13.97 seconds (5893.97 seconds total)