Starting phenix.real_space_refine on Sun Jun 29 06:36:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zgc_60075/06_2025/8zgc_60075.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zgc_60075/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zgc_60075/06_2025/8zgc_60075.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zgc_60075/06_2025/8zgc_60075.map" model { file = "/net/cci-nas-00/data/ceres_data/8zgc_60075/06_2025/8zgc_60075.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zgc_60075/06_2025/8zgc_60075.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 29, 'HIS:plan': 23, 'TYR:plan': 32, 'ASN:plan1': 26, 'TRP:plan': 17, 'ASP:plan': 47, 'PHE:plan': 36, 'GLU:plan': 49, 'ARG:plan': 50} 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: {'GLN:plan1': 29, 'HIS:plan': 23, 'TYR:plan': 32, 'ASN:plan1': 26, 'TRP:plan': 17, 'ASP:plan': 47, 'PHE:plan': 36, 'GLU:plan': 49, 'ARG:plan': 50} 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: {'GLN:plan1': 19, 'ASP:plan': 38, 'TYR:plan': 24, 'ASN:plan1': 18, 'TRP:plan': 13, 'HIS:plan': 19, 'PHE:plan': 23, 'GLU:plan': 44, 'ARG:plan': 49} 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: {'GLN:plan1': 19, 'ASP:plan': 38, 'TYR:plan': 24, 'ASN:plan1': 18, 'TRP:plan': 13, 'HIS:plan': 19, 'PHE:plan': 23, 'GLU:plan': 44, 'ARG:plan': 49} 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: 22.76, per 1000 atoms: 0.67 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: 10.04 Conformation dependent library (CDL) restraints added in 5.8 seconds 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9760 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 60 sheets defined 34.0% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.45 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: 17.98 Time building geometry restraints manager: 11.56 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: 0.05 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: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.640 Check model and map are aligned: 0.290 Set scattering table: 0.350 Process input model: 90.020 Find NCS groups from input model: 3.300 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.240 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (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 TRP 0.052 0.001 TRP U 495 HIS 0.006 0.001 HIS V 310 PHE 0.022 0.001 PHE U 529 TYR 0.015 0.001 TYR U 253 ARG 0.010 0.000 ARG U 595 Details of bonding type rmsd link_NAG-ASN : bond 0.01567 ( 6) link_NAG-ASN : angle 4.30776 ( 18) link_BETA1-4 : bond 0.00118 ( 2) link_BETA1-4 : angle 1.33645 ( 6) hydrogen bonds : bond 0.19612 ( 1338) hydrogen bonds : angle 6.85983 ( 3762) SS BOND : bond 0.00997 ( 8) SS BOND : angle 2.47567 ( 16) covalent geometry : bond 0.00459 (34796) covalent geometry : angle 0.87456 (47724) *********************** 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 : 4.078 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: 0.4443 time to fit residues: 172.6479 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 : 4.027 ------------------------------------------------------------------------------- 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 432 optimal weight: 6.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 1.9990 chunk 132 optimal weight: 0.0170 chunk 261 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 50.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.0870 chunk 298 optimal weight: 50.0000 chunk 464 optimal weight: 7.9990 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 GLN ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 719 HIS U 384 GLN U 578 ASN ** V 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.173173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.146170 restraints weight = 75268.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.143878 restraints weight = 108660.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.139837 restraints weight = 88959.752| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 34812 Z= 0.163 Angle : 0.566 8.041 47764 Z= 0.304 Chirality : 0.045 0.203 5606 Planarity : 0.004 0.052 6456 Dihedral : 8.047 76.360 5898 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.59 % Favored : 94.30 % Rotamer: Outliers : 3.60 % Allowed : 25.70 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.12), residues: 5156 helix: 1.75 (0.14), residues: 1512 sheet: -1.47 (0.18), residues: 824 loop : -1.18 (0.12), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP U 495 HIS 0.007 0.001 HIS V 310 PHE 0.021 0.001 PHE V 529 TYR 0.025 0.001 TYR V 494 ARG 0.012 0.000 ARG U 595 Details of bonding type rmsd link_NAG-ASN : bond 0.00805 ( 6) link_NAG-ASN : angle 2.25967 ( 18) link_BETA1-4 : bond 0.00470 ( 2) link_BETA1-4 : angle 1.52359 ( 6) hydrogen bonds : bond 0.03974 ( 1338) hydrogen bonds : angle 5.00790 ( 3762) SS BOND : bond 0.00711 ( 8) SS BOND : angle 1.98902 ( 16) covalent geometry : bond 0.00379 (34796) covalent geometry : angle 0.56337 (47724) *********************** 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 316 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 234 time to evaluate : 3.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8186 (t) REVERT: A 306 GLN cc_start: 0.6845 (pm20) cc_final: 0.6318 (pm20) REVERT: A 417 MET cc_start: 0.7839 (tpt) cc_final: 0.7566 (tpt) REVERT: A 424 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7562 (tp) REVERT: A 624 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8701 (mm) REVERT: B 704 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7195 (mpp80) REVERT: U 58 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8040 (mt) REVERT: U 464 LEU cc_start: 0.6697 (tp) cc_final: 0.6346 (tp) REVERT: V 116 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7712 (tm-30) REVERT: V 358 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7352 (ttm) REVERT: V 568 VAL cc_start: 0.8130 (OUTLIER) cc_final: 0.7796 (p) outliers start: 82 outliers final: 41 residues processed: 297 average time/residue: 0.4193 time to fit residues: 211.1045 Evaluate side-chains 271 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 223 time to evaluate : 4.036 ------------------------------------------------------------------------------- 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 424 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 624 LEU 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 170 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 595 HIS Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 651 ASN Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 58 LEU Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 193 ASP 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 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 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 188 VAL Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 239 LEU Chi-restraints excluded: chain V residue 283 CYS Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 358 MET Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 406 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 479 optimal weight: 30.0000 chunk 292 optimal weight: 40.0000 chunk 352 optimal weight: 30.0000 chunk 507 optimal weight: 0.3980 chunk 91 optimal weight: 0.0170 chunk 104 optimal weight: 2.9990 chunk 409 optimal weight: 40.0000 chunk 185 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 403 optimal weight: 30.0000 chunk 156 optimal weight: 1.9990 overall best weight: 2.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 597 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.171257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.149280 restraints weight = 73195.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.143178 restraints weight = 78855.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.139990 restraints weight = 89729.407| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 34812 Z= 0.219 Angle : 0.594 7.706 47764 Z= 0.314 Chirality : 0.046 0.211 5606 Planarity : 0.004 0.062 6456 Dihedral : 7.748 77.774 5895 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.44 % Favored : 93.43 % Rotamer: Outliers : 5.71 % Allowed : 24.87 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.12), residues: 5156 helix: 1.84 (0.14), residues: 1512 sheet: -1.32 (0.18), residues: 788 loop : -1.21 (0.12), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP U 495 HIS 0.009 0.001 HIS V 310 PHE 0.029 0.002 PHE B 331 TYR 0.023 0.002 TYR U 253 ARG 0.011 0.000 ARG V 595 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 6) link_NAG-ASN : angle 1.97658 ( 18) link_BETA1-4 : bond 0.00029 ( 2) link_BETA1-4 : angle 1.93364 ( 6) hydrogen bonds : bond 0.03932 ( 1338) hydrogen bonds : angle 4.62689 ( 3762) SS BOND : bond 0.00923 ( 8) SS BOND : angle 1.96284 ( 16) covalent geometry : bond 0.00525 (34796) covalent geometry : angle 0.59125 (47724) *********************** 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 355 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 225 time to evaluate : 4.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6178 (tpt) REVERT: A 417 MET cc_start: 0.8101 (tpt) cc_final: 0.7852 (tpt) REVERT: A 574 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: A 624 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8733 (mm) REVERT: B 704 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7250 (mpp80) REVERT: U 58 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7982 (mt) REVERT: U 160 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7523 (m-30) REVERT: U 179 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8908 (mp) REVERT: U 464 LEU cc_start: 0.6525 (tp) cc_final: 0.6207 (tp) REVERT: U 472 MET cc_start: 0.7105 (tpt) cc_final: 0.6842 (tpt) REVERT: V 116 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7715 (tm-30) REVERT: V 464 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8410 (tt) REVERT: V 568 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7651 (p) outliers start: 130 outliers final: 78 residues processed: 339 average time/residue: 0.4505 time to fit residues: 257.7991 Evaluate side-chains 300 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 213 time to evaluate : 4.095 ------------------------------------------------------------------------------- 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 68 THR 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 269 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 506 LEU 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 699 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 458 VAL 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 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 704 ARG Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 732 MET 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 177 LEU Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 205 MET Chi-restraints excluded: chain U residue 214 THR Chi-restraints excluded: chain U residue 293 VAL 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 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 519 LEU Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 53 ARG Chi-restraints excluded: chain V residue 90 THR Chi-restraints excluded: chain V residue 97 THR Chi-restraints excluded: chain V residue 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 248 ARG Chi-restraints excluded: chain V residue 283 CYS 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 372 VAL Chi-restraints excluded: chain V residue 406 THR Chi-restraints excluded: chain V residue 410 LEU Chi-restraints excluded: chain V residue 455 VAL Chi-restraints excluded: chain V residue 464 LEU Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 488 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 230 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 474 optimal weight: 8.9990 chunk 99 optimal weight: 0.9990 chunk 466 optimal weight: 7.9990 chunk 268 optimal weight: 50.0000 chunk 424 optimal weight: 5.9990 chunk 427 optimal weight: 50.0000 chunk 120 optimal weight: 1.9990 chunk 504 optimal weight: 0.4980 chunk 251 optimal weight: 10.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 561 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.170942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.150198 restraints weight = 73306.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.146389 restraints weight = 91413.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.143621 restraints weight = 84134.603| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 34812 Z= 0.236 Angle : 0.599 12.173 47764 Z= 0.315 Chirality : 0.046 0.199 5606 Planarity : 0.004 0.066 6456 Dihedral : 7.629 84.249 5895 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.21 % Favored : 93.68 % Rotamer: Outliers : 6.41 % Allowed : 25.09 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.12), residues: 5156 helix: 1.82 (0.14), residues: 1516 sheet: -1.29 (0.19), residues: 788 loop : -1.28 (0.12), residues: 2852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP U 495 HIS 0.009 0.001 HIS V 310 PHE 0.029 0.002 PHE B 331 TYR 0.024 0.002 TYR U 253 ARG 0.004 0.000 ARG V 226 Details of bonding type rmsd link_NAG-ASN : bond 0.00607 ( 6) link_NAG-ASN : angle 1.93088 ( 18) link_BETA1-4 : bond 0.00089 ( 2) link_BETA1-4 : angle 2.08794 ( 6) hydrogen bonds : bond 0.03675 ( 1338) hydrogen bonds : angle 4.47682 ( 3762) SS BOND : bond 0.00857 ( 8) SS BOND : angle 2.32978 ( 16) covalent geometry : bond 0.00569 (34796) covalent geometry : angle 0.59640 (47724) *********************** 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 370 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 224 time to evaluate : 3.919 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 152 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6081 (tp30) REVERT: A 376 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6132 (tpt) REVERT: A 417 MET cc_start: 0.8130 (tpt) cc_final: 0.7761 (tpt) REVERT: A 624 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8686 (mm) REVERT: B 112 ASP cc_start: 0.8000 (t0) cc_final: 0.7644 (t0) REVERT: U 42 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8177 (ttp80) REVERT: U 58 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7983 (mt) REVERT: U 179 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8856 (mp) REVERT: U 213 ARG cc_start: 0.8018 (tpp-160) cc_final: 0.7494 (ttm170) REVERT: U 272 SER cc_start: 0.9065 (OUTLIER) cc_final: 0.8815 (t) REVERT: U 464 LEU cc_start: 0.6651 (tp) cc_final: 0.6350 (tp) REVERT: U 472 MET cc_start: 0.7107 (tpt) cc_final: 0.6843 (tpt) REVERT: U 518 MET cc_start: 0.4818 (tpt) cc_final: 0.4372 (tpt) REVERT: V 116 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7734 (tm-30) REVERT: V 365 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7773 (mt0) REVERT: V 366 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: V 464 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8347 (tt) REVERT: V 544 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7618 (mmt90) REVERT: V 568 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7589 (p) outliers start: 146 outliers final: 94 residues processed: 353 average time/residue: 0.5870 time to fit residues: 346.3712 Evaluate side-chains 323 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 217 time to evaluate : 5.052 ------------------------------------------------------------------------------- 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 152 GLU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 461 ILE 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 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 698 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 CYS 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 458 VAL Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 526 LEU Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 581 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 732 MET 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 179 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 205 MET Chi-restraints excluded: chain U residue 214 THR Chi-restraints excluded: chain U residue 226 ARG 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 428 LEU Chi-restraints excluded: chain U residue 466 TYR Chi-restraints excluded: chain U residue 484 VAL Chi-restraints excluded: chain U residue 494 TYR Chi-restraints excluded: chain U residue 501 ILE Chi-restraints excluded: chain V residue 69 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 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 241 ASP Chi-restraints excluded: chain V residue 248 ARG Chi-restraints excluded: chain V residue 262 SER Chi-restraints excluded: chain V residue 283 CYS Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 300 THR Chi-restraints excluded: chain V residue 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 455 VAL Chi-restraints excluded: chain V residue 464 LEU Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 488 VAL Chi-restraints excluded: chain V residue 521 VAL Chi-restraints excluded: chain V residue 544 ARG Chi-restraints excluded: chain V residue 568 VAL Chi-restraints excluded: chain V residue 577 TRP Chi-restraints excluded: chain V residue 587 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 294 optimal weight: 10.0000 chunk 494 optimal weight: 50.0000 chunk 45 optimal weight: 9.9990 chunk 300 optimal weight: 8.9990 chunk 54 optimal weight: 0.3980 chunk 1 optimal weight: 9.9990 chunk 223 optimal weight: 1.9990 chunk 175 optimal weight: 0.0770 chunk 199 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 overall best weight: 2.2944 ------------------------------------------------------------------------------- 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 536 ASN A 561 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN ** U 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 169 ASN V 486 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.170377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.146618 restraints weight = 72890.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.142762 restraints weight = 94076.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.138888 restraints weight = 76527.562| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 34812 Z= 0.201 Angle : 0.572 11.212 47764 Z= 0.300 Chirality : 0.045 0.192 5606 Planarity : 0.004 0.064 6456 Dihedral : 7.330 81.963 5895 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.21 % Favored : 93.66 % Rotamer: Outliers : 6.41 % Allowed : 25.62 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.12), residues: 5156 helix: 1.90 (0.14), residues: 1512 sheet: -1.27 (0.19), residues: 788 loop : -1.28 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP U 495 HIS 0.008 0.001 HIS V 310 PHE 0.025 0.002 PHE B 331 TYR 0.023 0.002 TYR V 494 ARG 0.004 0.000 ARG V 471 Details of bonding type rmsd link_NAG-ASN : bond 0.00560 ( 6) link_NAG-ASN : angle 1.84466 ( 18) link_BETA1-4 : bond 0.00100 ( 2) link_BETA1-4 : angle 2.08243 ( 6) hydrogen bonds : bond 0.03367 ( 1338) hydrogen bonds : angle 4.32132 ( 3762) SS BOND : bond 0.00784 ( 8) SS BOND : angle 2.64268 ( 16) covalent geometry : bond 0.00483 (34796) covalent geometry : angle 0.56882 (47724) *********************** 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 365 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 219 time to evaluate : 4.022 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 152 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6263 (tp30) REVERT: A 376 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6127 (tpt) REVERT: A 417 MET cc_start: 0.8151 (tpt) cc_final: 0.7647 (tpt) REVERT: A 574 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: A 624 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8718 (mm) REVERT: B 112 ASP cc_start: 0.7906 (t0) cc_final: 0.7699 (t0) REVERT: B 704 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7246 (mpp80) REVERT: U 42 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8168 (ttp80) REVERT: U 58 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7985 (mt) REVERT: U 179 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8872 (mp) REVERT: U 213 ARG cc_start: 0.8052 (tpp-160) cc_final: 0.7707 (tpp-160) REVERT: U 272 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8850 (t) REVERT: U 326 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7261 (ptm-80) REVERT: U 464 LEU cc_start: 0.6783 (tp) cc_final: 0.6466 (tp) REVERT: U 472 MET cc_start: 0.7402 (tpt) cc_final: 0.7121 (tpt) REVERT: V 253 TYR cc_start: 0.7361 (t80) cc_final: 0.6991 (t80) REVERT: V 464 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8428 (tt) REVERT: V 544 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7570 (mmt90) REVERT: V 568 VAL cc_start: 0.7910 (OUTLIER) cc_final: 0.7639 (p) outliers start: 146 outliers final: 103 residues processed: 348 average time/residue: 0.4459 time to fit residues: 260.1503 Evaluate side-chains 332 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 216 time to evaluate : 4.130 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain A residue 152 GLU 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 424 LEU Chi-restraints excluded: chain A residue 458 VAL 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 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 699 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 230 VAL 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 308 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 526 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 681 HIS Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 704 ARG Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 732 MET 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 121 GLU Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 205 MET Chi-restraints excluded: chain U residue 214 THR 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 300 THR Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 325 SER Chi-restraints excluded: chain U residue 326 ARG 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 466 TYR 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 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 203 CYS Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 239 LEU Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 248 ARG Chi-restraints excluded: chain V residue 262 SER Chi-restraints excluded: chain V residue 283 CYS Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 300 THR Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 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 521 VAL Chi-restraints excluded: chain V residue 544 ARG Chi-restraints excluded: chain V residue 546 LEU Chi-restraints excluded: chain V residue 568 VAL Chi-restraints excluded: chain V residue 587 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 160 optimal weight: 0.8980 chunk 288 optimal weight: 40.0000 chunk 485 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 chunk 316 optimal weight: 9.9990 chunk 466 optimal weight: 9.9990 chunk 338 optimal weight: 8.9990 chunk 412 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 501 optimal weight: 10.0000 chunk 370 optimal weight: 50.0000 overall best weight: 6.1788 ------------------------------------------------------------------------------- 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 536 ASN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 HIS ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 148 GLN ** U 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 486 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.169077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.144260 restraints weight = 74744.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.141312 restraints weight = 108062.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.138849 restraints weight = 97254.399| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.156 34812 Z= 0.511 Angle : 0.864 11.032 47764 Z= 0.451 Chirality : 0.055 0.303 5606 Planarity : 0.006 0.088 6456 Dihedral : 8.191 83.454 5895 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.92 % Favored : 90.90 % Rotamer: Outliers : 7.25 % Allowed : 25.62 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.12), residues: 5156 helix: 1.18 (0.14), residues: 1528 sheet: -1.40 (0.20), residues: 692 loop : -1.73 (0.11), residues: 2936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP V 117 HIS 0.013 0.002 HIS V 235 PHE 0.051 0.003 PHE B 331 TYR 0.036 0.003 TYR B 268 ARG 0.007 0.001 ARG B 239 Details of bonding type rmsd link_NAG-ASN : bond 0.00945 ( 6) link_NAG-ASN : angle 2.39085 ( 18) link_BETA1-4 : bond 0.00349 ( 2) link_BETA1-4 : angle 3.19622 ( 6) hydrogen bonds : bond 0.05309 ( 1338) hydrogen bonds : angle 5.02242 ( 3762) SS BOND : bond 0.01278 ( 8) SS BOND : angle 3.05157 ( 16) covalent geometry : bond 0.01232 (34796) covalent geometry : angle 0.86015 (47724) *********************** 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 387 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 222 time to evaluate : 4.143 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: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6059 (tpt) REVERT: A 417 MET cc_start: 0.7966 (tpt) cc_final: 0.7524 (tpt) REVERT: A 624 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8759 (mm) REVERT: U 179 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8978 (mp) REVERT: U 213 ARG cc_start: 0.8060 (tpp-160) cc_final: 0.7763 (tpp-160) REVERT: U 326 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7397 (ptm-80) REVERT: V 253 TYR cc_start: 0.7661 (t80) cc_final: 0.7394 (t80) REVERT: V 464 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8328 (tt) outliers start: 165 outliers final: 129 residues processed: 373 average time/residue: 0.4311 time to fit residues: 270.6806 Evaluate side-chains 349 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 215 time to evaluate : 3.732 ------------------------------------------------------------------------------- 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 117 ILE Chi-restraints excluded: chain A residue 132 SER 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 424 LEU Chi-restraints excluded: chain A residue 445 VAL 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 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 43 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 274 THR 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 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 526 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 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 704 ARG Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 724 THR 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 55 LEU 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 179 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 194 SER Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 205 MET Chi-restraints excluded: chain U residue 214 THR Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 247 SER Chi-restraints excluded: chain U residue 272 SER Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 325 SER Chi-restraints excluded: chain U residue 326 ARG 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 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 181 ILE Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 203 CYS Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 239 LEU Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 248 ARG Chi-restraints excluded: chain V residue 262 SER Chi-restraints excluded: chain V residue 283 CYS Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 300 THR Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 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 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 116 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 255 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 440 optimal weight: 30.0000 chunk 283 optimal weight: 50.0000 chunk 56 optimal weight: 20.0000 chunk 385 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 561 GLN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 ASN ** U 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 578 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.173398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.148553 restraints weight = 74809.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.146666 restraints weight = 107917.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.143482 restraints weight = 96929.617| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34812 Z= 0.142 Angle : 0.566 10.639 47764 Z= 0.296 Chirality : 0.045 0.170 5606 Planarity : 0.004 0.068 6456 Dihedral : 7.425 80.810 5895 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.51 % Favored : 94.36 % Rotamer: Outliers : 5.27 % Allowed : 27.81 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.12), residues: 5156 helix: 1.68 (0.14), residues: 1528 sheet: -1.39 (0.19), residues: 756 loop : -1.48 (0.11), residues: 2872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP U 495 HIS 0.007 0.001 HIS V 310 PHE 0.021 0.001 PHE V 529 TYR 0.025 0.001 TYR U 253 ARG 0.005 0.000 ARG V 370 Details of bonding type rmsd link_NAG-ASN : bond 0.00669 ( 6) link_NAG-ASN : angle 1.99357 ( 18) link_BETA1-4 : bond 0.00138 ( 2) link_BETA1-4 : angle 2.06274 ( 6) hydrogen bonds : bond 0.03179 ( 1338) hydrogen bonds : angle 4.33750 ( 3762) SS BOND : bond 0.00702 ( 8) SS BOND : angle 2.30143 ( 16) covalent geometry : bond 0.00337 (34796) covalent geometry : angle 0.56332 (47724) *********************** 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 340 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 220 time to evaluate : 4.136 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 265 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8693 (tp) REVERT: A 417 MET cc_start: 0.8047 (tpt) cc_final: 0.7413 (tpt) REVERT: A 624 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8638 (mm) REVERT: A 732 MET cc_start: 0.7686 (tpp) cc_final: 0.7200 (tpp) REVERT: B 112 ASP cc_start: 0.7941 (t0) cc_final: 0.7696 (t0) REVERT: U 42 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8227 (ttp80) REVERT: U 58 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8020 (mt) REVERT: U 179 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8834 (mp) REVERT: U 213 ARG cc_start: 0.8029 (tpp-160) cc_final: 0.7683 (tpp-160) REVERT: U 285 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8798 (mttt) REVERT: U 326 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7311 (ptm-80) REVERT: U 464 LEU cc_start: 0.6768 (tp) cc_final: 0.6480 (tp) REVERT: V 253 TYR cc_start: 0.7257 (t80) cc_final: 0.6958 (t80) REVERT: V 366 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: V 464 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8322 (tt) REVERT: V 487 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8722 (mt) REVERT: V 544 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7653 (mmt90) REVERT: V 568 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7626 (p) outliers start: 120 outliers final: 76 residues processed: 325 average time/residue: 0.4567 time to fit residues: 248.2527 Evaluate side-chains 304 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 216 time to evaluate : 4.060 ------------------------------------------------------------------------------- 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 252 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 323 TYR 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 476 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 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 116 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 285 ASP 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 418 LEU Chi-restraints excluded: chain B residue 432 LEU 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 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 732 MET 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 179 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 272 SER Chi-restraints excluded: chain U residue 285 LYS 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 326 ARG 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 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 283 CYS Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 366 GLU 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 544 ARG Chi-restraints excluded: chain V residue 568 VAL Chi-restraints excluded: chain V residue 577 TRP Chi-restraints excluded: chain V residue 587 ASP Chi-restraints excluded: chain V residue 591 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 335 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 438 optimal weight: 50.0000 chunk 324 optimal weight: 40.0000 chunk 274 optimal weight: 40.0000 chunk 322 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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** A 680 ASN U 65 HIS V 148 GLN V 486 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.170899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.148728 restraints weight = 72424.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.143478 restraints weight = 83529.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.141071 restraints weight = 78943.115| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34812 Z= 0.143 Angle : 0.553 10.845 47764 Z= 0.287 Chirality : 0.044 0.209 5606 Planarity : 0.004 0.059 6456 Dihedral : 7.066 80.965 5894 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.99 % Favored : 93.87 % Rotamer: Outliers : 5.14 % Allowed : 27.99 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.12), residues: 5156 helix: 1.87 (0.14), residues: 1512 sheet: -1.27 (0.19), residues: 756 loop : -1.38 (0.11), residues: 2888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP U 577 HIS 0.006 0.001 HIS V 310 PHE 0.022 0.001 PHE V 529 TYR 0.022 0.001 TYR U 253 ARG 0.003 0.000 ARG V 370 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 6) link_NAG-ASN : angle 1.79755 ( 18) link_BETA1-4 : bond 0.00111 ( 2) link_BETA1-4 : angle 2.12594 ( 6) hydrogen bonds : bond 0.03013 ( 1338) hydrogen bonds : angle 4.18594 ( 3762) SS BOND : bond 0.00670 ( 8) SS BOND : angle 2.12382 ( 16) covalent geometry : bond 0.00341 (34796) covalent geometry : angle 0.55035 (47724) *********************** 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 342 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 225 time to evaluate : 3.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.5886 (tpt) REVERT: A 417 MET cc_start: 0.8172 (tpt) cc_final: 0.7543 (tpt) REVERT: A 624 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8711 (mm) REVERT: A 732 MET cc_start: 0.7538 (tpp) cc_final: 0.7076 (tpp) REVERT: B 112 ASP cc_start: 0.8008 (t0) cc_final: 0.7686 (t0) REVERT: B 704 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7317 (mpp80) REVERT: U 179 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8831 (mp) REVERT: U 213 ARG cc_start: 0.8054 (tpp-160) cc_final: 0.7712 (tpp-160) REVERT: U 326 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7314 (ptm-80) REVERT: U 464 LEU cc_start: 0.6810 (tp) cc_final: 0.6501 (tp) REVERT: U 519 LEU cc_start: 0.5865 (OUTLIER) cc_final: 0.5583 (pp) REVERT: V 253 TYR cc_start: 0.7238 (t80) cc_final: 0.6882 (t80) REVERT: V 291 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8958 (pt) REVERT: V 366 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: V 464 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8358 (tt) REVERT: V 544 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7706 (mmt90) REVERT: V 568 VAL cc_start: 0.7912 (OUTLIER) cc_final: 0.7685 (p) outliers start: 117 outliers final: 87 residues processed: 328 average time/residue: 0.4211 time to fit residues: 230.9877 Evaluate side-chains 316 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 218 time to evaluate : 3.721 ------------------------------------------------------------------------------- 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 265 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 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 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 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 116 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 285 ASP 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 418 LEU Chi-restraints excluded: chain B residue 432 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 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 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 179 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 214 THR Chi-restraints excluded: chain U residue 218 ILE Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 325 SER Chi-restraints excluded: chain U residue 326 ARG 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 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 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 239 LEU Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 262 SER Chi-restraints excluded: chain V residue 283 CYS Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 366 GLU 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 486 ASN Chi-restraints excluded: chain V residue 521 VAL Chi-restraints excluded: chain V residue 544 ARG Chi-restraints excluded: chain V residue 568 VAL Chi-restraints excluded: chain V residue 577 TRP Chi-restraints excluded: chain V residue 587 ASP Chi-restraints excluded: chain V residue 591 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 382 optimal weight: 0.0040 chunk 37 optimal weight: 2.9990 chunk 416 optimal weight: 40.0000 chunk 313 optimal weight: 20.0000 chunk 431 optimal weight: 10.0000 chunk 289 optimal weight: 40.0000 chunk 386 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 371 optimal weight: 0.0070 chunk 179 optimal weight: 0.9980 overall best weight: 0.9812 ------------------------------------------------------------------------------- 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** A 717 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.174683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.149776 restraints weight = 75540.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.147315 restraints weight = 106975.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.144698 restraints weight = 97630.198| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34812 Z= 0.113 Angle : 0.532 11.039 47764 Z= 0.275 Chirality : 0.044 0.194 5606 Planarity : 0.004 0.053 6456 Dihedral : 6.757 81.198 5894 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.22 % Favored : 94.65 % Rotamer: Outliers : 4.48 % Allowed : 28.65 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.12), residues: 5156 helix: 1.91 (0.14), residues: 1528 sheet: -1.17 (0.20), residues: 756 loop : -1.35 (0.11), residues: 2872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP U 577 HIS 0.006 0.001 HIS V 310 PHE 0.021 0.001 PHE V 529 TYR 0.023 0.001 TYR V 492 ARG 0.005 0.000 ARG V 485 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 6) link_NAG-ASN : angle 1.72858 ( 18) link_BETA1-4 : bond 0.00177 ( 2) link_BETA1-4 : angle 1.96959 ( 6) hydrogen bonds : bond 0.02737 ( 1338) hydrogen bonds : angle 4.04139 ( 3762) SS BOND : bond 0.00643 ( 8) SS BOND : angle 2.06495 ( 16) covalent geometry : bond 0.00265 (34796) covalent geometry : angle 0.52896 (47724) *********************** 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 327 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 225 time to evaluate : 3.683 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: 0.5276 (OUTLIER) cc_final: 0.4091 (mt-10) REVERT: A 265 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8683 (tp) REVERT: A 376 MET cc_start: 0.7036 (OUTLIER) cc_final: 0.5841 (tpt) REVERT: A 417 MET cc_start: 0.8153 (tpt) cc_final: 0.7527 (tpt) REVERT: A 624 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8672 (mm) REVERT: A 652 PHE cc_start: 0.7362 (p90) cc_final: 0.6692 (p90) REVERT: A 732 MET cc_start: 0.7497 (tpp) cc_final: 0.7042 (tpp) REVERT: B 112 ASP cc_start: 0.7921 (t0) cc_final: 0.7624 (t0) REVERT: B 704 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7340 (mpp80) REVERT: U 42 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8143 (ttp80) REVERT: U 179 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8766 (mp) REVERT: U 213 ARG cc_start: 0.8006 (tpp-160) cc_final: 0.7701 (tpp-160) REVERT: U 326 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7259 (ptm-80) REVERT: U 464 LEU cc_start: 0.6676 (tp) cc_final: 0.6374 (tp) REVERT: U 518 MET cc_start: 0.4802 (tpt) cc_final: 0.4581 (tpt) REVERT: V 253 TYR cc_start: 0.7071 (t80) cc_final: 0.6762 (t80) REVERT: V 291 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8803 (pt) REVERT: V 366 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: V 464 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8360 (tt) REVERT: V 544 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7697 (mmt90) outliers start: 102 outliers final: 77 residues processed: 314 average time/residue: 0.4484 time to fit residues: 235.8318 Evaluate side-chains 310 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 221 time to evaluate : 3.796 ------------------------------------------------------------------------------- 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 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 282 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 536 ASN 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 170 ILE Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 349 GLN Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 432 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 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 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 179 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 194 SER Chi-restraints excluded: chain U residue 218 ILE Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 325 SER Chi-restraints excluded: chain U residue 326 ARG 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 162 ILE Chi-restraints excluded: chain V residue 168 ASP Chi-restraints excluded: chain V residue 181 ILE Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 203 CYS Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 239 LEU Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 243 ARG Chi-restraints excluded: chain V residue 283 CYS 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 366 GLU 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 544 ARG 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 368 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 250 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 300 optimal weight: 40.0000 chunk 160 optimal weight: 0.1980 chunk 210 optimal weight: 1.9990 chunk 335 optimal weight: 30.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 169 ASN V 486 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.175059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.150401 restraints weight = 75269.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.147803 restraints weight = 108949.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.145228 restraints weight = 99641.018| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 34812 Z= 0.104 Angle : 0.523 11.320 47764 Z= 0.269 Chirality : 0.043 0.184 5606 Planarity : 0.004 0.052 6456 Dihedral : 6.490 81.602 5894 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.00 % Favored : 94.86 % Rotamer: Outliers : 4.53 % Allowed : 28.16 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.12), residues: 5156 helix: 2.00 (0.14), residues: 1532 sheet: -1.12 (0.19), residues: 796 loop : -1.29 (0.12), residues: 2828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP U 495 HIS 0.005 0.001 HIS V 310 PHE 0.021 0.001 PHE V 529 TYR 0.018 0.001 TYR U 253 ARG 0.003 0.000 ARG V 370 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 6) link_NAG-ASN : angle 1.65115 ( 18) link_BETA1-4 : bond 0.00257 ( 2) link_BETA1-4 : angle 1.83034 ( 6) hydrogen bonds : bond 0.02551 ( 1338) hydrogen bonds : angle 3.94500 ( 3762) SS BOND : bond 0.00614 ( 8) SS BOND : angle 2.00859 ( 16) covalent geometry : bond 0.00240 (34796) covalent geometry : angle 0.52064 (47724) ********************** 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 336 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 233 time to evaluate : 4.015 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: 0.5211 (OUTLIER) cc_final: 0.4177 (mt-10) REVERT: A 376 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.5872 (tpt) REVERT: A 417 MET cc_start: 0.8209 (tpt) cc_final: 0.7575 (tpt) REVERT: B 112 ASP cc_start: 0.7830 (t0) cc_final: 0.7565 (t0) REVERT: B 704 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7331 (mpp80) REVERT: U 179 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8749 (mp) REVERT: U 213 ARG cc_start: 0.8002 (tpp-160) cc_final: 0.7746 (tpp-160) REVERT: U 326 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7113 (ptm-80) REVERT: U 464 LEU cc_start: 0.6512 (tp) cc_final: 0.6203 (tp) REVERT: V 253 TYR cc_start: 0.6987 (t80) cc_final: 0.6687 (t80) REVERT: V 291 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8573 (pt) REVERT: V 366 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: V 464 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8370 (tt) REVERT: V 544 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7710 (mmt90) outliers start: 103 outliers final: 80 residues processed: 323 average time/residue: 0.4302 time to fit residues: 234.3061 Evaluate side-chains 314 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 225 time to evaluate : 4.246 ------------------------------------------------------------------------------- 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 73 GLU 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 282 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 536 ASN Chi-restraints excluded: chain A residue 551 ARG Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 698 CYS 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 170 ILE 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 349 GLN Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 433 SER 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 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 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 177 LEU Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 194 SER Chi-restraints excluded: chain U residue 218 ILE 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 326 ARG 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 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 243 ARG Chi-restraints excluded: chain V residue 262 SER Chi-restraints excluded: chain V residue 283 CYS Chi-restraints excluded: chain V residue 291 LEU Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 315 VAL Chi-restraints excluded: chain V residue 328 ILE Chi-restraints excluded: chain V residue 366 GLU 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 486 ASN Chi-restraints excluded: chain V residue 521 VAL Chi-restraints excluded: chain V residue 544 ARG 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 407 optimal weight: 10.0000 chunk 329 optimal weight: 50.0000 chunk 57 optimal weight: 20.0000 chunk 423 optimal weight: 20.0000 chunk 323 optimal weight: 50.0000 chunk 46 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 315 optimal weight: 10.0000 chunk 278 optimal weight: 50.0000 chunk 43 optimal weight: 4.9990 overall best weight: 4.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.174271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.151457 restraints weight = 75557.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.147336 restraints weight = 92298.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.144514 restraints weight = 93003.352| |-----------------------------------------------------------------------------| r_work (final): 0.4136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.162 34812 Z= 0.259 Angle : 0.674 59.200 47764 Z= 0.382 Chirality : 0.050 1.016 5606 Planarity : 0.004 0.148 6456 Dihedral : 6.498 81.613 5894 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.06 % Favored : 94.80 % Rotamer: Outliers : 4.09 % Allowed : 28.43 % Favored : 67.49 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.12), residues: 5156 helix: 1.95 (0.14), residues: 1532 sheet: -1.11 (0.19), residues: 796 loop : -1.30 (0.12), residues: 2828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP U 495 HIS 0.005 0.001 HIS V 310 PHE 0.022 0.001 PHE V 529 TYR 0.019 0.002 TYR U 217 ARG 0.004 0.000 ARG U 53 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 6) link_NAG-ASN : angle 1.63852 ( 18) link_BETA1-4 : bond 0.00477 ( 2) link_BETA1-4 : angle 2.03192 ( 6) hydrogen bonds : bond 0.02780 ( 1338) hydrogen bonds : angle 3.95037 ( 3762) SS BOND : bond 0.01158 ( 8) SS BOND : angle 2.37961 ( 16) covalent geometry : bond 0.00575 (34796) covalent geometry : angle 0.67165 (47724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11039.12 seconds wall clock time: 192 minutes 31.63 seconds (11551.63 seconds total)