Starting phenix.real_space_refine on Sun Jun 29 04:54:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zgg_60078/06_2025/8zgg_60078.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zgg_60078/06_2025/8zgg_60078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zgg_60078/06_2025/8zgg_60078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zgg_60078/06_2025/8zgg_60078.map" model { file = "/net/cci-nas-00/data/ceres_data/8zgg_60078/06_2025/8zgg_60078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zgg_60078/06_2025/8zgg_60078.cif" } resolution = 3.75 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= 0.049 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 4 7.51 5 Fe 2 7.16 5 P 8 5.49 5 S 100 5.16 5 C 21194 2.51 5 N 6299 2.21 5 O 6537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 34144 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: "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: "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: "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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 51 Unusual residues: {' MN': 1, 'AKG': 1, 'FE2': 1, 'NAG': 1, 'UDP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' MN': 1, '660': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' MN': 1, '660': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.84, per 1000 atoms: 0.64 Number of scatterers: 34144 At special positions: 0 Unit cell: (178.2, 227.7, 239.8, 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 4 24.99 S 100 16.00 P 8 15.00 O 6537 8.00 N 6299 7.00 C 21194 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=2.06 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 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: 8.91 Conformation dependent library (CDL) restraints added in 5.1 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: 166 helices and 57 sheets defined 32.9% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.90 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: 3.882A pdb=" N PHE A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 4.028A pdb=" N VAL A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 101 removed outlier: 3.787A 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: 3.522A pdb=" N ALA A 151 " --> pdb=" O TRP A 148 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU A 152 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 191 through 201 removed outlier: 3.839A 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 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 258 through 266 Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 324 through 328 removed outlier: 3.653A pdb=" N VAL A 328 " --> pdb=" O PRO A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' 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: 3.630A pdb=" N GLU A 364 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A 365 " --> pdb=" O PRO A 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 365' Processing helix chain 'A' and resid 367 through 381 Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.754A pdb=" N ASN A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 449 removed outlier: 3.775A 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: 3.729A pdb=" N LYS A 500 " --> pdb=" O SER A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.638A pdb=" N TRP A 531 " --> pdb=" O PRO A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 544 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 Processing helix chain 'A' and resid 631 through 639 Processing helix chain 'B' and resid 49 through 61 removed outlier: 3.561A pdb=" N LEU B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 98 removed outlier: 4.560A pdb=" N VAL B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) removed outlier: 3.842A 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 153 removed outlier: 3.973A pdb=" N GLU B 152 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 182 removed outlier: 4.353A pdb=" N GLN B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 200 removed outlier: 3.509A pdb=" N TYR B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 258 through 267 removed outlier: 3.908A pdb=" N LEU B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN B 267 " --> pdb=" O ASN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 319 removed outlier: 4.083A pdb=" N LEU B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 339 through 354 removed outlier: 3.604A 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 361 through 365 removed outlier: 3.902A pdb=" N GLU B 364 " --> pdb=" O GLY B 361 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 365 " --> pdb=" O PRO B 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 361 through 365' Processing helix chain 'B' and resid 367 through 381 Processing helix chain 'B' and resid 401 through 410 removed outlier: 3.918A pdb=" N ASN B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 449 removed outlier: 3.516A pdb=" N GLN B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 475 removed outlier: 3.537A 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 545 Processing helix chain 'B' and resid 548 through 555 Processing helix chain 'B' and resid 573 through 588 removed outlier: 3.590A pdb=" N TYR B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) removed outlier: 4.094A 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: 4.075A pdb=" N MET B 634 " --> pdb=" O TYR B 630 " (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 removed outlier: 3.511A pdb=" N PHE C 62 " --> pdb=" O SER C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 97 removed outlier: 3.995A pdb=" N VAL C 90 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG C 91 " --> pdb=" O GLY C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 133 Processing helix chain 'C' and resid 148 through 152 removed outlier: 4.023A 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 191 through 201 removed outlier: 3.759A pdb=" N ASP C 201 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 209 Processing helix chain 'C' and resid 258 through 266 Processing helix chain 'C' and resid 310 through 319 removed outlier: 4.007A 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 removed outlier: 3.752A pdb=" N GLU C 364 " --> pdb=" O GLY C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 382 Processing helix chain 'C' and resid 401 through 410 removed outlier: 4.043A pdb=" N ASN C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) 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 532 Processing helix chain 'C' and resid 536 through 545 Processing helix chain 'C' and resid 548 through 555 removed outlier: 3.526A pdb=" N GLY C 555 " --> pdb=" O ARG C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 588 Processing helix chain 'C' and resid 614 through 618 Processing helix chain 'C' and resid 619 through 630 Processing helix chain 'C' and resid 630 through 639 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 63 Processing helix chain 'D' and resid 86 through 97 removed outlier: 3.662A pdb=" N VAL D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 133 removed outlier: 3.587A pdb=" N GLY D 133 " --> pdb=" O PHE D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 152 removed outlier: 3.510A 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: 4.050A pdb=" N PHE D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP D 201 " --> pdb=" O ARG D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 209 Processing helix chain 'D' and resid 258 through 267 Processing helix chain 'D' and resid 310 through 319 removed outlier: 3.942A pdb=" N LEU D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) 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 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 410 removed outlier: 3.918A pdb=" N ASN D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 449 removed outlier: 3.643A pdb=" N GLN D 449 " --> pdb=" O VAL D 445 " (cutoff:3.500A) 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 532 Processing helix chain 'D' and resid 536 through 545 Processing helix chain 'D' and resid 546 through 555 removed outlier: 4.328A pdb=" N SER D 550 " --> pdb=" O HIS D 546 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG D 551 " --> pdb=" O GLU D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 588 removed outlier: 3.687A pdb=" N GLY D 588 " --> pdb=" O MET D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 618 Processing helix chain 'D' and resid 619 through 630 Processing helix chain 'D' and resid 630 through 639 removed outlier: 3.632A pdb=" N MET D 634 " --> pdb=" O TYR D 630 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 76 removed outlier: 3.557A pdb=" N THR U 70 " --> pdb=" O ALA U 66 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG U 76 " --> pdb=" O GLY U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 109 removed outlier: 3.531A pdb=" N VAL U 100 " --> pdb=" O ASN U 96 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA U 107 " --> pdb=" O GLU U 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 149 removed outlier: 3.830A pdb=" N GLU U 141 " --> pdb=" O ASP U 137 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N HIS U 142 " --> pdb=" O SER U 138 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS U 145 " --> pdb=" O GLU U 141 " (cutoff:3.500A) Processing helix chain 'U' and resid 175 through 182 removed outlier: 3.648A pdb=" N LEU U 179 " --> pdb=" O ASP U 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 216 through 222 Processing helix chain 'U' and resid 266 through 273 Processing helix chain 'U' and resid 300 through 317 removed outlier: 3.635A pdb=" N GLU U 304 " --> pdb=" O THR U 300 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET U 316 " --> pdb=" O GLN U 312 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL U 317 " --> pdb=" O LEU U 313 " (cutoff:3.500A) Processing helix chain 'U' and resid 352 through 365 removed outlier: 3.711A pdb=" N GLU U 356 " --> pdb=" O GLN U 352 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG U 357 " --> pdb=" O ASP U 353 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N MET U 358 " --> pdb=" O ARG U 354 " (cutoff:3.500A) Processing helix chain 'U' and resid 381 through 388 removed outlier: 3.520A pdb=" N ALA U 387 " --> pdb=" O SER U 383 " (cutoff:3.500A) 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: 3.793A pdb=" N GLU U 513 " --> pdb=" O LEU U 509 " (cutoff:3.500A) Processing helix chain 'U' and resid 520 through 528 Proline residue: U 526 - end of helix Processing helix chain 'U' and resid 534 through 541 removed outlier: 3.918A pdb=" N LYS U 538 " --> pdb=" O VAL U 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 75 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: 3.529A pdb=" N ARG V 248 " --> pdb=" O ALA V 245 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN V 249 " --> pdb=" O ALA V 246 " (cutoff:3.500A) Processing helix chain 'V' and resid 267 through 275 Processing helix chain 'V' and resid 300 through 317 removed outlier: 3.544A pdb=" N GLU V 304 " --> pdb=" O THR V 300 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET V 316 " --> pdb=" O GLN V 312 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL V 317 " --> pdb=" O LEU V 313 " (cutoff:3.500A) Processing helix chain 'V' and resid 352 through 365 removed outlier: 3.735A pdb=" N GLU V 356 " --> pdb=" O GLN V 352 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG V 357 " --> pdb=" O ASP V 353 " (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: 3.871A pdb=" N LYS V 538 " --> pdb=" O VAL V 534 " (cutoff:3.500A) Processing helix chain 'W' and resid 66 through 75 removed outlier: 3.593A pdb=" N ALA W 73 " --> pdb=" O THR W 69 " (cutoff:3.500A) Processing helix chain 'W' and resid 96 through 108 Processing helix chain 'W' and resid 136 through 157 removed outlier: 3.654A pdb=" N MET W 157 " --> pdb=" O SER W 153 " (cutoff:3.500A) Processing helix chain 'W' and resid 175 through 182 Processing helix chain 'W' and resid 216 through 222 Processing helix chain 'W' and resid 244 through 250 removed outlier: 3.557A pdb=" N LEU W 250 " --> pdb=" O SER W 247 " (cutoff:3.500A) Processing helix chain 'W' and resid 264 through 276 removed outlier: 4.267A pdb=" N PHE W 269 " --> pdb=" O ASP W 265 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA W 270 " --> pdb=" O ILE W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 300 through 319 removed outlier: 4.487A pdb=" N LYS W 318 " --> pdb=" O GLU W 314 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS W 319 " --> pdb=" O VAL W 315 " (cutoff:3.500A) Processing helix chain 'W' and resid 352 through 365 Processing helix chain 'W' and resid 381 through 386 removed outlier: 3.962A pdb=" N GLU W 386 " --> pdb=" O THR W 382 " (cutoff:3.500A) 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 513 Processing helix chain 'W' and resid 520 through 529 Proline residue: W 526 - end of helix Processing helix chain 'W' and resid 534 through 541 removed outlier: 4.024A 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 removed outlier: 3.671A pdb=" N THR X 84 " --> pdb=" O ARG X 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 108 Processing helix chain 'X' and resid 136 through 157 removed outlier: 3.720A pdb=" N MET X 157 " --> pdb=" O SER X 153 " (cutoff:3.500A) Processing helix chain 'X' and resid 175 through 180 Processing helix chain 'X' and resid 181 through 184 removed outlier: 4.124A pdb=" N ASN X 184 " --> pdb=" O ILE X 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 181 through 184' Processing helix chain 'X' and resid 216 through 222 Processing helix chain 'X' and resid 244 through 249 removed outlier: 3.660A pdb=" N ASN X 249 " --> pdb=" O ALA X 246 " (cutoff:3.500A) Processing helix chain 'X' and resid 267 through 275 Processing helix chain 'X' and resid 300 through 319 removed outlier: 3.522A pdb=" N GLU X 304 " --> pdb=" O THR X 300 " (cutoff:3.500A) removed outlier: 4.295A 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 381 through 388 removed outlier: 3.657A pdb=" N ALA X 387 " --> pdb=" O SER X 383 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU X 388 " --> pdb=" O GLN X 384 " (cutoff:3.500A) 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 513 Processing helix chain 'X' and resid 520 through 529 Proline residue: X 526 - end of helix Processing helix chain 'X' and resid 534 through 541 removed outlier: 4.122A 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: 7.951A pdb=" N ARG A 67 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N VAL A 41 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU A 69 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR A 43 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 40 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET A 109 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 111 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 44 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE A 163 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 141 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 139 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLY A 167 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N LEU A 137 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU A 136 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP A 213 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.045A 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: 3.703A pdb=" N ILE A 117 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 252 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLN A 220 " --> pdb=" O HIS A 253 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 229 through 232 Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 300 removed outlier: 3.796A pdb=" N TYR A 465 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 332 through 333 removed outlier: 7.291A pdb=" N LEU A 332 " --> pdb=" O VAL A 360 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 455 through 457 Processing sheet with id=AA7, first strand: chain 'A' and resid 567 through 570 removed outlier: 5.497A pdb=" N TRP A 707 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 678 " --> pdb=" O TRP A 707 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 676 " --> pdb=" O LEU A 709 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS A 711 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE A 673 " --> pdb=" O VAL A 736 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 736 " --> pdb=" O PHE A 673 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA9, first strand: chain 'A' and resid 698 through 699 Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 67 removed outlier: 8.213A pdb=" N ARG B 67 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 41 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 111 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 139 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N GLY B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N LEU B 137 " --> pdb=" O GLY B 167 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASP B 213 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 116 through 118 Processing sheet with id=AB3, first strand: chain 'B' and resid 229 through 233 Processing sheet with id=AB4, first strand: chain 'B' and resid 328 through 329 removed outlier: 7.232A pdb=" N VAL B 298 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N HIS B 333 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 302 " --> pdb=" O HIS B 333 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 328 through 329 removed outlier: 7.232A pdb=" N VAL B 298 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 389 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B 303 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR B 465 " --> pdb=" O SER B 390 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 395 through 396 Processing sheet with id=AB7, first strand: chain 'B' and resid 431 through 432 removed outlier: 3.535A pdb=" N ALA B 431 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 455 through 457 removed outlier: 3.794A pdb=" N LEU B 506 " --> pdb=" O TRP B 456 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 567 through 570 removed outlier: 5.233A pdb=" N TRP B 707 " --> pdb=" O ALA B 678 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 678 " --> pdb=" O TRP B 707 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS B 711 " --> pdb=" O THR B 674 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE B 673 " --> pdb=" O VAL B 736 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 736 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET B 650 " --> pdb=" O PHE B 735 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL B 653 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 612 " --> pdb=" O VAL B 653 " (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 'C' and resid 66 through 69 removed outlier: 8.114A pdb=" N ARG C 67 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL C 41 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU C 69 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR C 43 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL C 44 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C 171 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 163 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER C 139 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N GLY C 167 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 11.727A pdb=" N LEU C 137 " --> pdb=" O GLY C 167 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU C 136 " --> pdb=" O ASN C 211 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 116 through 118 removed outlier: 6.207A pdb=" N GLN C 220 " --> pdb=" O HIS C 253 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 229 through 233 Processing sheet with id=AC6, first strand: chain 'C' and resid 356 through 360 removed outlier: 4.156A pdb=" N ALA C 356 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C 298 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N PHE C 331 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU C 300 " --> pdb=" O PHE C 331 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N HIS C 333 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL C 302 " --> pdb=" O HIS C 333 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 301 " --> pdb=" O PHE C 389 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C 303 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 413 " --> pdb=" O HIS C 505 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N SER C 507 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA C 415 " --> pdb=" O SER C 507 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU C 504 " --> pdb=" O VAL C 458 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 396 through 397 removed outlier: 3.888A pdb=" N SER C 419 " --> pdb=" O GLY C 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 431 through 432 Processing sheet with id=AC9, first strand: chain 'C' and resid 569 through 570 removed outlier: 6.189A pdb=" N TRP C 707 " --> pdb=" O ALA C 678 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA C 678 " --> pdb=" O TRP C 707 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 673 " --> pdb=" O VAL C 736 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 736 " --> pdb=" O PHE C 673 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 675 " --> pdb=" O SER C 734 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET C 650 " --> pdb=" O PHE C 735 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 686 through 688 Processing sheet with id=AD2, first strand: chain 'D' and resid 66 through 69 removed outlier: 8.212A pdb=" N ARG D 67 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL D 41 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU D 69 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N THR D 43 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU D 40 " --> pdb=" O MET D 109 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL D 111 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE D 42 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER D 139 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N GLY D 167 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 11.330A pdb=" N LEU D 137 " --> pdb=" O GLY D 167 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU D 136 " --> pdb=" O ASN D 211 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 116 through 118 removed outlier: 3.500A pdb=" N VAL D 252 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLN D 220 " --> pdb=" O HIS D 253 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 230 through 232 Processing sheet with id=AD5, first strand: chain 'D' and resid 328 through 329 removed outlier: 6.788A pdb=" N VAL D 298 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N HIS D 333 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL D 302 " --> pdb=" O HIS D 333 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 360 " --> pdb=" O LEU D 332 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 328 through 329 removed outlier: 6.788A pdb=" N VAL D 298 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N PHE D 299 " --> pdb=" O PHE D 389 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU D 391 " --> pdb=" O PHE D 299 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA D 301 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 414 " --> pdb=" O VAL D 466 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 431 through 432 removed outlier: 4.217A pdb=" N ALA D 431 " --> pdb=" O ALA D 439 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 456 through 457 removed outlier: 3.567A pdb=" N LEU D 506 " --> pdb=" O TRP D 456 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 567 through 570 removed outlier: 6.345A pdb=" N TRP D 707 " --> pdb=" O ALA D 678 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA D 678 " --> pdb=" O TRP D 707 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS D 711 " --> pdb=" O THR D 674 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 675 " --> pdb=" O SER D 734 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D 734 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET D 650 " --> pdb=" O PHE D 735 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 653 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE D 612 " --> pdb=" O VAL D 653 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 686 through 687 Processing sheet with id=AE2, first strand: chain 'D' and resid 691 through 693 Processing sheet with id=AE3, first strand: chain 'U' and resid 115 through 120 removed outlier: 8.953A pdb=" N GLU U 116 " --> pdb=" O THR U 84 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU U 86 " --> pdb=" O GLU U 116 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ARG U 118 " --> pdb=" O LEU U 86 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL U 88 " --> pdb=" O ARG U 118 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N ALA U 120 " --> pdb=" O VAL U 88 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N THR U 90 " --> pdb=" O ALA U 120 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU U 58 " --> pdb=" O TRP U 87 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU U 55 " --> pdb=" O LEU U 163 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL U 187 " --> pdb=" O TYR U 281 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N CYS U 283 " --> pdb=" O VAL U 187 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ALA U 189 " --> pdb=" O CYS U 283 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL U 282 " --> pdb=" O PHE U 229 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 170 through 171 Processing sheet with id=AE5, first strand: chain 'U' and resid 342 through 343 removed outlier: 3.708A pdb=" N GLU U 342 " --> pdb=" O LYS U 430 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE U 501 " --> pdb=" O SER U 431 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL U 433 " --> pdb=" O TYR U 499 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR U 499 " --> pdb=" O VAL U 433 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 346 through 347 removed outlier: 3.678A pdb=" N ASN U 347 " --> pdb=" O VAL U 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'U' and resid 439 through 440 Processing sheet with id=AE8, first strand: chain 'V' and resid 85 through 86 Processing sheet with id=AE9, first strand: chain 'V' and resid 162 through 163 removed outlier: 3.516A pdb=" N VAL V 188 " --> pdb=" O LEU V 239 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL V 187 " --> pdb=" O TYR V 281 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'V' and resid 170 through 171 Processing sheet with id=AF2, first strand: chain 'V' and resid 372 through 374 removed outlier: 6.228A pdb=" N VAL V 372 " --> pdb=" O VAL V 343 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N MET V 345 " --> pdb=" O VAL V 372 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA V 374 " --> pdb=" O MET V 345 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN V 347 " --> pdb=" O ALA V 374 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLU V 342 " --> pdb=" O LEU V 432 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N PHE V 434 " --> pdb=" O GLU V 342 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N PHE V 344 " --> pdb=" O PHE V 434 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL V 433 " --> pdb=" O TYR V 499 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR V 499 " --> pdb=" O VAL V 433 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR V 496 " --> pdb=" O ARG V 469 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ARG V 469 " --> pdb=" O THR V 496 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA V 498 " --> pdb=" O VAL V 467 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL V 467 " --> pdb=" O ALA V 498 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE V 465 " --> pdb=" O VAL V 500 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'V' and resid 439 through 440 removed outlier: 3.502A pdb=" N TYR V 557 " --> pdb=" O ARG V 439 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'V' and resid 487 through 489 Processing sheet with id=AF5, first strand: chain 'W' and resid 114 through 115 removed outlier: 7.219A pdb=" N ALA W 89 " --> pdb=" O ILE W 56 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LEU W 58 " --> pdb=" O ALA W 89 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ASP W 91 " --> pdb=" O LEU W 58 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA W 60 " --> pdb=" O ASP W 91 " (cutoff:3.500A) removed outlier: 6.952A 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: 6.221A pdb=" N LEU W 55 " --> pdb=" O LEU W 163 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL W 165 " --> pdb=" O LEU W 55 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA W 57 " --> pdb=" O VAL W 165 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE W 238 " --> pdb=" O PHE W 164 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL W 187 " --> pdb=" O TYR W 281 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N CYS W 283 " --> pdb=" O VAL W 187 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA W 189 " --> pdb=" O CYS W 283 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'W' and resid 170 through 171 Processing sheet with id=AF8, first strand: chain 'W' and resid 201 through 202 removed outlier: 3.603A pdb=" N MET W 233 " --> pdb=" O TRP W 202 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 370 through 373 removed outlier: 6.110A pdb=" N VAL W 343 " --> pdb=" O ARG W 370 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL W 372 " --> pdb=" O VAL W 343 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N MET W 345 " --> pdb=" O VAL W 372 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU W 342 " --> pdb=" O LYS W 430 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR W 499 " --> pdb=" O VAL W 433 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR W 496 " --> pdb=" O ARG W 469 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ARG W 469 " --> pdb=" O THR W 496 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA W 498 " --> pdb=" O VAL W 467 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL W 467 " --> pdb=" O ALA W 498 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE W 549 " --> pdb=" O LEU W 464 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 439 through 440 Processing sheet with id=AG2, first strand: chain 'X' and resid 239 through 240 removed outlier: 3.629A pdb=" N VAL X 188 " --> pdb=" O LEU X 239 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N CYS X 283 " --> pdb=" O VAL X 187 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA X 189 " --> pdb=" O CYS X 283 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 370 through 371 removed outlier: 5.456A pdb=" N VAL X 343 " --> pdb=" O ARG X 370 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU X 342 " --> pdb=" O LYS X 430 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE X 434 " --> pdb=" O PHE X 344 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE X 501 " --> pdb=" O SER X 431 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL X 433 " --> pdb=" O TYR X 499 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR X 499 " --> pdb=" O VAL X 433 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE X 465 " --> pdb=" O VAL X 500 " (cutoff:3.500A) 1207 hydrogen bonds defined for protein. 3417 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: 14.94 Time building geometry restraints manager: 10.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 6425 1.32 - 1.47: 13791 1.47 - 1.62: 14332 1.62 - 1.77: 14 1.77 - 1.92: 168 Bond restraints: 34730 Sorted by residual: bond pdb=" C3 660 V 701 " pdb=" C4 660 V 701 " ideal model delta sigma weight residual 1.522 1.244 0.278 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C3 660 U 701 " pdb=" C4 660 U 701 " ideal model delta sigma weight residual 1.522 1.250 0.272 2.00e-02 2.50e+03 1.85e+02 bond pdb=" C4 660 U 701 " pdb=" O6 660 U 701 " ideal model delta sigma weight residual 1.432 1.680 -0.248 2.00e-02 2.50e+03 1.53e+02 bond pdb=" C4 660 V 701 " pdb=" O6 660 V 701 " ideal model delta sigma weight residual 1.432 1.672 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" O5' UDP B 805 " pdb=" PA UDP B 805 " ideal model delta sigma weight residual 1.581 1.757 -0.176 1.50e-02 4.44e+03 1.38e+02 ... (remaining 34725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 47369 3.93 - 7.86: 201 7.86 - 11.79: 40 11.79 - 15.73: 10 15.73 - 19.66: 5 Bond angle restraints: 47625 Sorted by residual: angle pdb=" O5' UDP A 804 " pdb=" PA UDP A 804 " pdb=" O2A UDP A 804 " ideal model delta sigma weight residual 110.83 96.44 14.39 1.00e+00 1.00e+00 2.07e+02 angle pdb=" O1A UDP A 804 " pdb=" PA UDP A 804 " pdb=" O3A UDP A 804 " ideal model delta sigma weight residual 109.95 122.88 -12.93 1.00e+00 1.00e+00 1.67e+02 angle pdb=" O5' UDP B 805 " pdb=" PA UDP B 805 " pdb=" O2A UDP B 805 " ideal model delta sigma weight residual 110.83 99.45 11.38 1.00e+00 1.00e+00 1.30e+02 angle pdb=" O3A UDP A 804 " pdb=" PB UDP A 804 " pdb=" O3B UDP A 804 " ideal model delta sigma weight residual 112.01 100.80 11.21 1.00e+00 1.00e+00 1.26e+02 angle pdb=" O1A UDP B 805 " pdb=" PA UDP B 805 " pdb=" O3A UDP B 805 " ideal model delta sigma weight residual 109.95 120.32 -10.37 1.00e+00 1.00e+00 1.08e+02 ... (remaining 47620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.36: 19539 26.36 - 52.72: 1021 52.72 - 79.08: 157 79.08 - 105.44: 43 105.44 - 131.80: 21 Dihedral angle restraints: 20781 sinusoidal: 5745 harmonic: 15036 Sorted by residual: dihedral pdb=" CB CYS A 279 " pdb=" SG CYS A 279 " pdb=" SG CYS A 282 " pdb=" CB CYS A 282 " ideal model delta sinusoidal sigma weight residual 93.00 174.28 -81.28 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" CB CYS U 228 " pdb=" SG CYS U 228 " pdb=" SG CYS U 283 " pdb=" CB CYS U 283 " ideal model delta sinusoidal sigma weight residual 93.00 20.15 72.85 1 1.00e+01 1.00e-02 6.77e+01 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 -26.28 -59.72 1 1.00e+01 1.00e-02 4.76e+01 ... (remaining 20778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 4931 0.071 - 0.142: 631 0.142 - 0.213: 23 0.213 - 0.284: 5 0.284 - 0.356: 3 Chirality restraints: 5593 Sorted by residual: chirality pdb=" CA ASP U 91 " pdb=" N ASP U 91 " pdb=" C ASP U 91 " pdb=" CB ASP U 91 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" C41 660 V 701 " pdb=" C40 660 V 701 " pdb=" C45 660 V 701 " pdb=" O36 660 V 701 " both_signs ideal model delta sigma weight residual False -2.28 -2.59 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C41 660 U 701 " pdb=" C40 660 U 701 " pdb=" C45 660 U 701 " pdb=" O36 660 U 701 " both_signs ideal model delta sigma weight residual False -2.28 -2.58 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 5590 not shown) Planarity restraints: 6458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 382 " -0.118 5.00e-02 4.00e+02 1.74e-01 4.84e+01 pdb=" N PRO B 383 " 0.301 5.00e-02 4.00e+02 pdb=" CA PRO B 383 " -0.098 5.00e-02 4.00e+02 pdb=" CD PRO B 383 " -0.085 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU U 58 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C LEU U 58 " 0.063 2.00e-02 2.50e+03 pdb=" O LEU U 58 " -0.024 2.00e-02 2.50e+03 pdb=" N LEU U 59 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU V 58 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" C LEU V 58 " 0.044 2.00e-02 2.50e+03 pdb=" O LEU V 58 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU V 59 " -0.015 2.00e-02 2.50e+03 ... (remaining 6455 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 534 2.66 - 3.22: 31984 3.22 - 3.78: 49502 3.78 - 4.34: 59891 4.34 - 4.90: 100269 Nonbonded interactions: 242180 Sorted by model distance: nonbonded pdb=" OH TYR V 259 " pdb=" O SER V 262 " model vdw 2.105 3.040 nonbonded pdb=" OH TYR U 259 " pdb=" O SER U 262 " model vdw 2.145 3.040 nonbonded pdb=" OG SER B 671 " pdb=" O VAL B 736 " model vdw 2.154 3.040 nonbonded pdb=" OE1 GLN A 625 " pdb=" OG1 THR A 629 " model vdw 2.171 3.040 nonbonded pdb=" NH1 ARG U 53 " pdb=" OD2 ASP U 160 " model vdw 2.175 3.120 ... (remaining 242175 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: 0.00 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: 4.570 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: 0.030 Extract box with map and model: 1.350 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 82.670 Find NCS groups from input model: 3.060 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 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 0.278 34745 Z= 0.290 Angle : 0.789 19.658 47662 Z= 0.427 Chirality : 0.046 0.356 5593 Planarity : 0.005 0.174 6453 Dihedral : 17.645 131.800 10997 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.72 % Favored : 94.16 % Rotamer: Outliers : 0.62 % Allowed : 28.69 % Favored : 70.69 % Cbeta Deviations : 0.02 % 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: -1.15 (0.12), residues: 5156 helix: 1.38 (0.14), residues: 1504 sheet: -1.63 (0.20), residues: 756 loop : -1.76 (0.11), residues: 2896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP V 117 HIS 0.005 0.001 HIS A 719 PHE 0.025 0.002 PHE B 281 TYR 0.024 0.001 TYR U 211 ARG 0.008 0.001 ARG A 287 Details of bonding type rmsd link_NAG-ASN : bond 0.00475 ( 5) link_NAG-ASN : angle 3.15663 ( 15) link_BETA1-4 : bond 0.00386 ( 2) link_BETA1-4 : angle 1.49000 ( 6) hydrogen bonds : bond 0.20089 ( 1205) hydrogen bonds : angle 6.76737 ( 3417) SS BOND : bond 0.01516 ( 8) SS BOND : angle 3.44160 ( 16) covalent geometry : bond 0.00542 (34730) covalent geometry : angle 0.78438 (47625) *********************** 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 278 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 264 time to evaluate : 3.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 208 LEU cc_start: 0.8043 (mm) cc_final: 0.7664 (mp) REVERT: U 90 THR cc_start: 0.8681 (OUTLIER) cc_final: 0.8442 (p) REVERT: U 91 ASP cc_start: 0.7652 (t70) cc_final: 0.7393 (t0) REVERT: U 137 ASP cc_start: 0.8348 (t0) cc_final: 0.8146 (t70) REVERT: U 327 PHE cc_start: 0.7520 (m-80) cc_final: 0.7218 (m-80) REVERT: U 345 MET cc_start: 0.6159 (mmm) cc_final: 0.5892 (mmm) REVERT: U 518 MET cc_start: 0.1491 (mmp) cc_final: 0.0398 (mmp) REVERT: V 144 MET cc_start: 0.7302 (ttm) cc_final: 0.6975 (mtt) REVERT: V 358 MET cc_start: 0.7286 (mtm) cc_final: 0.7037 (ttm) outliers start: 14 outliers final: 4 residues processed: 277 average time/residue: 0.4249 time to fit residues: 201.5506 Evaluate side-chains 254 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 249 time to evaluate : 3.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain U residue 90 THR Chi-restraints excluded: chain U residue 239 LEU Chi-restraints excluded: chain U residue 312 GLN Chi-restraints excluded: chain V residue 226 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 432 optimal weight: 10.0000 chunk 388 optimal weight: 0.5980 chunk 215 optimal weight: 30.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 207 optimal weight: 50.0000 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 8.9990 chunk 298 optimal weight: 1.9990 chunk 464 optimal weight: 7.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS B 681 HIS B 719 HIS ** V 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 540 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.179108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.156892 restraints weight = 71189.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.154789 restraints weight = 94760.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.151970 restraints weight = 81242.560| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 34745 Z= 0.313 Angle : 0.719 11.674 47662 Z= 0.370 Chirality : 0.049 0.242 5593 Planarity : 0.005 0.120 6453 Dihedral : 11.050 111.100 5809 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.84 % Favored : 91.08 % Rotamer: Outliers : 6.02 % Allowed : 25.79 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.22 (0.12), residues: 5156 helix: 1.28 (0.14), residues: 1516 sheet: -1.54 (0.20), residues: 772 loop : -1.84 (0.11), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP V 117 HIS 0.009 0.001 HIS V 113 PHE 0.028 0.002 PHE U 238 TYR 0.026 0.002 TYR A 465 ARG 0.006 0.001 ARG A 287 Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 5) link_NAG-ASN : angle 3.06430 ( 15) link_BETA1-4 : bond 0.00632 ( 2) link_BETA1-4 : angle 1.87085 ( 6) hydrogen bonds : bond 0.04796 ( 1205) hydrogen bonds : angle 5.14055 ( 3417) SS BOND : bond 0.01596 ( 8) SS BOND : angle 3.26356 ( 16) covalent geometry : bond 0.00754 (34730) covalent geometry : angle 0.71468 (47625) *********************** 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 376 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 239 time to evaluate : 6.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 107 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8965 (mt) REVERT: B 208 LEU cc_start: 0.8130 (mm) cc_final: 0.7540 (mp) REVERT: B 376 MET cc_start: 0.8725 (mtm) cc_final: 0.8337 (mtm) REVERT: B 497 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.7591 (t80) REVERT: B 568 TRP cc_start: 0.8108 (OUTLIER) cc_final: 0.6712 (t60) REVERT: B 681 HIS cc_start: 0.8058 (OUTLIER) cc_final: 0.7399 (m-70) REVERT: U 358 MET cc_start: 0.7578 (mmt) cc_final: 0.6992 (mmt) REVERT: U 518 MET cc_start: 0.1473 (mmp) cc_final: 0.0895 (mmp) REVERT: V 116 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: V 122 GLU cc_start: 0.7310 (mm-30) cc_final: 0.7058 (mm-30) REVERT: V 226 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8829 (mtt-85) REVERT: V 291 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8499 (pt) REVERT: V 380 MET cc_start: 0.6863 (ppp) cc_final: 0.5446 (ppp) REVERT: V 544 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6838 (mmt90) REVERT: V 598 GLN cc_start: 0.4750 (OUTLIER) cc_final: 0.4183 (pt0) outliers start: 137 outliers final: 62 residues processed: 361 average time/residue: 0.4968 time to fit residues: 309.7148 Evaluate side-chains 299 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 228 time to evaluate : 3.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 42 ILE 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 107 ILE Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 62 ASN Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 236 SER Chi-restraints excluded: chain U residue 268 VAL Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 312 GLN Chi-restraints excluded: chain U residue 343 VAL Chi-restraints excluded: chain U residue 350 ARG Chi-restraints excluded: chain U residue 397 ARG Chi-restraints excluded: chain U residue 555 LEU Chi-restraints excluded: chain U residue 556 ILE Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 116 GLU Chi-restraints excluded: chain V residue 162 ILE 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 220 ILE Chi-restraints excluded: chain V residue 226 ARG 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 300 THR Chi-restraints excluded: chain V residue 318 LYS Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 406 THR Chi-restraints excluded: chain V residue 442 ILE Chi-restraints excluded: chain V residue 466 TYR Chi-restraints excluded: chain V residue 510 LEU Chi-restraints excluded: chain V residue 544 ARG Chi-restraints excluded: chain V residue 598 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 439 optimal weight: 50.0000 chunk 211 optimal weight: 1.9990 chunk 52 optimal weight: 0.0570 chunk 496 optimal weight: 4.9990 chunk 173 optimal weight: 50.0000 chunk 498 optimal weight: 9.9990 chunk 399 optimal weight: 40.0000 chunk 35 optimal weight: 0.0970 chunk 385 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 487 optimal weight: 10.0000 overall best weight: 2.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS B 561 GLN B 595 HIS B 681 HIS U 365 GLN V 347 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.180379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.157785 restraints weight = 71261.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.154333 restraints weight = 89885.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.151330 restraints weight = 88149.314| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 34745 Z= 0.207 Angle : 0.623 11.336 47662 Z= 0.319 Chirality : 0.046 0.355 5593 Planarity : 0.004 0.092 6453 Dihedral : 9.655 106.028 5806 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.75 % Favored : 93.19 % Rotamer: Outliers : 5.54 % Allowed : 26.14 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.11 (0.12), residues: 5156 helix: 1.44 (0.14), residues: 1520 sheet: -1.56 (0.20), residues: 784 loop : -1.79 (0.11), residues: 2852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 623 HIS 0.006 0.001 HIS B 681 PHE 0.016 0.002 PHE B 428 TYR 0.018 0.001 TYR V 198 ARG 0.006 0.000 ARG A 287 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 5) link_NAG-ASN : angle 2.72201 ( 15) link_BETA1-4 : bond 0.00449 ( 2) link_BETA1-4 : angle 1.83334 ( 6) hydrogen bonds : bond 0.03705 ( 1205) hydrogen bonds : angle 4.66223 ( 3417) SS BOND : bond 0.01045 ( 8) SS BOND : angle 3.03500 ( 16) covalent geometry : bond 0.00494 (34730) covalent geometry : angle 0.61866 (47625) *********************** 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 363 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 237 time to evaluate : 3.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: B 112 ASP cc_start: 0.8594 (t0) cc_final: 0.8394 (t0) REVERT: B 497 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.7510 (t80) REVERT: B 568 TRP cc_start: 0.8178 (OUTLIER) cc_final: 0.6554 (t60) REVERT: B 584 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8143 (mmm) REVERT: B 681 HIS cc_start: 0.7988 (OUTLIER) cc_final: 0.7640 (m90) REVERT: U 344 PHE cc_start: 0.7993 (m-80) cc_final: 0.7555 (m-10) REVERT: U 596 GLU cc_start: 0.5357 (OUTLIER) cc_final: 0.4161 (pp20) REVERT: V 122 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6926 (mm-30) REVERT: V 177 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8662 (tp) REVERT: V 226 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.8828 (mtt-85) REVERT: V 316 MET cc_start: 0.7742 (ptp) cc_final: 0.7175 (ptp) REVERT: V 380 MET cc_start: 0.6901 (ppp) cc_final: 0.5974 (ppp) REVERT: V 544 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6898 (mmt90) REVERT: V 598 GLN cc_start: 0.4801 (OUTLIER) cc_final: 0.4225 (pt0) outliers start: 126 outliers final: 69 residues processed: 350 average time/residue: 0.4349 time to fit residues: 265.3932 Evaluate side-chains 312 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 233 time to evaluate : 4.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 SER 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 130 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain U residue 40 GLU Chi-restraints excluded: chain U residue 41 GLU Chi-restraints excluded: chain U residue 55 LEU Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 146 LEU Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 236 SER Chi-restraints excluded: chain U residue 237 THR Chi-restraints excluded: chain U residue 238 PHE Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 291 LEU Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 312 GLN Chi-restraints excluded: chain U residue 397 ARG Chi-restraints excluded: chain U residue 484 VAL Chi-restraints excluded: chain U residue 555 LEU Chi-restraints excluded: chain U residue 596 GLU Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 176 THR Chi-restraints excluded: chain V residue 177 LEU Chi-restraints excluded: chain V residue 203 CYS Chi-restraints excluded: chain V residue 214 THR Chi-restraints excluded: chain V residue 220 ILE Chi-restraints excluded: chain V residue 226 ARG Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 273 CYS Chi-restraints excluded: chain V residue 300 THR Chi-restraints excluded: chain V residue 311 VAL Chi-restraints excluded: chain V residue 358 MET Chi-restraints excluded: chain V residue 406 THR Chi-restraints excluded: chain V residue 474 VAL Chi-restraints excluded: chain V residue 476 HIS Chi-restraints excluded: chain V residue 544 ARG Chi-restraints excluded: chain V residue 598 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 171 optimal weight: 30.0000 chunk 468 optimal weight: 5.9990 chunk 479 optimal weight: 50.0000 chunk 371 optimal weight: 0.9990 chunk 170 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 406 optimal weight: 40.0000 chunk 319 optimal weight: 10.0000 chunk 398 optimal weight: 2.9990 chunk 219 optimal weight: 20.0000 overall best weight: 4.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS ** B 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 65 HIS ** U 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.178432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.157161 restraints weight = 70732.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.154520 restraints weight = 91445.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.150581 restraints weight = 86183.709| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.131 34745 Z= 0.393 Angle : 0.779 13.944 47662 Z= 0.400 Chirality : 0.051 0.412 5593 Planarity : 0.006 0.091 6453 Dihedral : 9.948 114.819 5806 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.95 % Favored : 89.97 % Rotamer: Outliers : 7.56 % Allowed : 25.40 % Favored : 67.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.31 (0.12), residues: 5156 helix: 1.37 (0.14), residues: 1492 sheet: -1.80 (0.19), residues: 852 loop : -1.89 (0.11), residues: 2812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP V 117 HIS 0.013 0.002 HIS U 256 PHE 0.037 0.003 PHE B 428 TYR 0.030 0.002 TYR A 465 ARG 0.007 0.001 ARG V 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00506 ( 5) link_NAG-ASN : angle 2.82164 ( 15) link_BETA1-4 : bond 0.00391 ( 2) link_BETA1-4 : angle 2.42096 ( 6) hydrogen bonds : bond 0.04353 ( 1205) hydrogen bonds : angle 4.83099 ( 3417) SS BOND : bond 0.01816 ( 8) SS BOND : angle 3.02450 ( 16) covalent geometry : bond 0.00944 (34730) covalent geometry : angle 0.77564 (47625) *********************** 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 407 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 235 time to evaluate : 3.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: B 73 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.5870 (mt-10) REVERT: B 323 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.5508 (m-80) REVERT: B 376 MET cc_start: 0.8775 (ttm) cc_final: 0.8357 (mtm) REVERT: B 497 PHE cc_start: 0.8498 (OUTLIER) cc_final: 0.7637 (t80) REVERT: B 568 TRP cc_start: 0.8313 (OUTLIER) cc_final: 0.5718 (t60) REVERT: B 681 HIS cc_start: 0.8197 (OUTLIER) cc_final: 0.7845 (m170) REVERT: U 94 MET cc_start: 0.7946 (ppp) cc_final: 0.7679 (ppp) REVERT: U 309 MET cc_start: 0.7227 (mtt) cc_final: 0.7011 (mtm) REVERT: U 344 PHE cc_start: 0.8001 (m-80) cc_final: 0.7659 (m-10) REVERT: U 518 MET cc_start: 0.1543 (mmp) cc_final: 0.0904 (mmp) REVERT: U 561 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.6282 (m-80) REVERT: V 226 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8869 (mtt-85) REVERT: V 291 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8327 (pt) REVERT: V 380 MET cc_start: 0.7064 (ppp) cc_final: 0.6714 (ppp) REVERT: V 544 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7067 (mmt90) REVERT: V 598 GLN cc_start: 0.4834 (OUTLIER) cc_final: 0.4342 (pt0) outliers start: 172 outliers final: 111 residues processed: 394 average time/residue: 0.4042 time to fit residues: 270.7852 Evaluate side-chains 346 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 224 time to evaluate : 4.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain U residue 40 GLU Chi-restraints excluded: chain U residue 41 GLU Chi-restraints excluded: chain U residue 55 LEU Chi-restraints excluded: chain U residue 62 ASN Chi-restraints excluded: chain U residue 146 LEU Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 191 MET Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 236 SER Chi-restraints excluded: chain U residue 237 THR Chi-restraints excluded: chain U residue 238 PHE Chi-restraints excluded: chain U residue 239 LEU Chi-restraints excluded: chain U residue 241 ASP Chi-restraints excluded: chain U residue 268 VAL Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 291 LEU 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 312 GLN Chi-restraints excluded: chain U residue 343 VAL Chi-restraints excluded: chain U residue 350 ARG Chi-restraints excluded: chain U residue 397 ARG Chi-restraints excluded: chain U residue 438 LEU Chi-restraints excluded: chain U residue 466 TYR Chi-restraints excluded: chain U residue 484 VAL Chi-restraints excluded: chain U residue 525 LEU Chi-restraints excluded: chain U residue 555 LEU Chi-restraints excluded: chain U residue 561 TYR Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 162 ILE 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 220 ILE Chi-restraints excluded: chain V residue 226 ARG Chi-restraints excluded: chain V residue 239 LEU Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 273 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 334 THR Chi-restraints excluded: chain V residue 372 VAL Chi-restraints excluded: chain V residue 406 THR Chi-restraints excluded: chain V residue 424 VAL Chi-restraints excluded: chain V residue 442 ILE Chi-restraints excluded: chain V residue 466 TYR Chi-restraints excluded: chain V residue 502 SER Chi-restraints excluded: chain V residue 510 LEU Chi-restraints excluded: chain V residue 536 GLU Chi-restraints excluded: chain V residue 544 ARG Chi-restraints excluded: chain V residue 576 VAL Chi-restraints excluded: chain V residue 598 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 427 optimal weight: 40.0000 chunk 464 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 496 optimal weight: 0.0870 chunk 126 optimal weight: 8.9990 chunk 438 optimal weight: 6.9990 chunk 503 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 283 optimal weight: 1.9990 chunk 380 optimal weight: 0.7980 chunk 499 optimal weight: 6.9990 overall best weight: 2.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS B 595 HIS B 668 HIS B 681 HIS ** U 256 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 = 0.4518 r_free = 0.4518 target = 0.180451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.158244 restraints weight = 70712.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.155099 restraints weight = 90519.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.152074 restraints weight = 88167.032| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 34745 Z= 0.199 Angle : 0.624 13.815 47662 Z= 0.318 Chirality : 0.046 0.399 5593 Planarity : 0.004 0.085 6453 Dihedral : 8.802 98.023 5806 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.04 % Favored : 92.88 % Rotamer: Outliers : 6.20 % Allowed : 27.28 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.11 (0.12), residues: 5156 helix: 1.57 (0.14), residues: 1500 sheet: -1.66 (0.19), residues: 816 loop : -1.80 (0.11), residues: 2840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP V 117 HIS 0.018 0.001 HIS U 256 PHE 0.019 0.002 PHE U 238 TYR 0.017 0.001 TYR V 198 ARG 0.006 0.000 ARG U 485 Details of bonding type rmsd link_NAG-ASN : bond 0.00361 ( 5) link_NAG-ASN : angle 2.49481 ( 15) link_BETA1-4 : bond 0.00388 ( 2) link_BETA1-4 : angle 2.04834 ( 6) hydrogen bonds : bond 0.03392 ( 1205) hydrogen bonds : angle 4.47524 ( 3417) SS BOND : bond 0.01097 ( 8) SS BOND : angle 2.56038 ( 16) covalent geometry : bond 0.00476 (34730) covalent geometry : angle 0.62048 (47625) *********************** 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 379 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 238 time to evaluate : 3.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: B 323 TYR cc_start: 0.7757 (OUTLIER) cc_final: 0.5250 (m-80) REVERT: B 376 MET cc_start: 0.8588 (ttm) cc_final: 0.8105 (mtm) REVERT: B 403 LEU cc_start: 0.8574 (tp) cc_final: 0.8194 (tp) REVERT: B 424 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8757 (tp) REVERT: B 497 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7550 (t80) REVERT: B 568 TRP cc_start: 0.8304 (OUTLIER) cc_final: 0.5397 (t60) REVERT: B 681 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.7561 (m-70) REVERT: U 233 MET cc_start: 0.8701 (tpp) cc_final: 0.8378 (tpt) REVERT: U 344 PHE cc_start: 0.7933 (m-80) cc_final: 0.7705 (m-80) REVERT: U 417 TYR cc_start: 0.5598 (OUTLIER) cc_final: 0.4809 (m-80) REVERT: U 518 MET cc_start: 0.1508 (mmp) cc_final: 0.0508 (mmp) REVERT: V 177 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8706 (tp) REVERT: V 226 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.8927 (mtt-85) REVERT: V 291 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8281 (pt) REVERT: V 380 MET cc_start: 0.6940 (ppp) cc_final: 0.6637 (ppp) REVERT: V 544 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.7084 (mmt90) REVERT: V 598 GLN cc_start: 0.4724 (OUTLIER) cc_final: 0.4211 (pt0) outliers start: 141 outliers final: 99 residues processed: 367 average time/residue: 0.4026 time to fit residues: 254.5542 Evaluate side-chains 341 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 230 time to evaluate : 3.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 243 VAL 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 377 ASP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain U residue 40 GLU Chi-restraints excluded: chain U residue 41 GLU Chi-restraints excluded: chain U residue 55 LEU Chi-restraints excluded: chain U residue 62 ASN Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 146 LEU Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 236 SER Chi-restraints excluded: chain U residue 237 THR Chi-restraints excluded: chain U residue 238 PHE Chi-restraints excluded: chain U residue 268 VAL Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 291 LEU Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 312 GLN Chi-restraints excluded: chain U residue 343 VAL Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 417 TYR Chi-restraints excluded: chain U residue 466 TYR Chi-restraints excluded: chain U residue 484 VAL Chi-restraints excluded: chain U residue 527 VAL Chi-restraints excluded: chain U residue 555 LEU Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 163 LEU Chi-restraints excluded: chain V residue 176 THR Chi-restraints excluded: chain V residue 177 LEU 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 220 ILE Chi-restraints excluded: chain V residue 226 ARG Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 273 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 318 LYS Chi-restraints excluded: chain V residue 334 THR 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 442 ILE Chi-restraints excluded: chain V residue 463 ASP Chi-restraints excluded: chain V residue 502 SER Chi-restraints excluded: chain V residue 510 LEU Chi-restraints excluded: chain V residue 536 GLU Chi-restraints excluded: chain V residue 544 ARG Chi-restraints excluded: chain V residue 576 VAL Chi-restraints excluded: chain V residue 598 GLN Chi-restraints excluded: chain V residue 612 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 401 optimal weight: 6.9990 chunk 361 optimal weight: 0.7980 chunk 497 optimal weight: 50.0000 chunk 173 optimal weight: 50.0000 chunk 350 optimal weight: 0.6980 chunk 246 optimal weight: 20.0000 chunk 238 optimal weight: 0.9980 chunk 439 optimal weight: 5.9990 chunk 360 optimal weight: 0.8980 chunk 411 optimal weight: 8.9990 chunk 469 optimal weight: 9.9990 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 ASN ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS B 595 HIS B 681 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.182464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.160106 restraints weight = 69919.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.156943 restraints weight = 88799.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.153594 restraints weight = 87761.082| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34745 Z= 0.182 Angle : 0.607 12.679 47662 Z= 0.308 Chirality : 0.046 0.346 5593 Planarity : 0.004 0.077 6453 Dihedral : 8.146 94.195 5806 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.93 % Favored : 91.97 % Rotamer: Outliers : 6.72 % Allowed : 26.63 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.01 (0.12), residues: 5156 helix: 1.68 (0.14), residues: 1500 sheet: -1.69 (0.19), residues: 848 loop : -1.72 (0.11), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 623 HIS 0.012 0.001 HIS U 256 PHE 0.025 0.002 PHE U 524 TYR 0.016 0.001 TYR V 198 ARG 0.006 0.000 ARG V 349 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 5) link_NAG-ASN : angle 2.33066 ( 15) link_BETA1-4 : bond 0.00599 ( 2) link_BETA1-4 : angle 1.97479 ( 6) hydrogen bonds : bond 0.03177 ( 1205) hydrogen bonds : angle 4.31123 ( 3417) SS BOND : bond 0.01243 ( 8) SS BOND : angle 2.61666 ( 16) covalent geometry : bond 0.00438 (34730) covalent geometry : angle 0.60372 (47625) *********************** 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 390 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 237 time to evaluate : 3.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 LEU cc_start: 0.7727 (tt) cc_final: 0.7458 (tt) REVERT: A 574 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: A 729 ARG cc_start: 0.5000 (OUTLIER) cc_final: 0.4554 (ptm160) REVERT: B 234 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: B 323 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.5262 (m-80) REVERT: B 376 MET cc_start: 0.8582 (ttm) cc_final: 0.8016 (mtm) REVERT: B 403 LEU cc_start: 0.8547 (tp) cc_final: 0.8139 (tp) REVERT: B 424 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8786 (tp) REVERT: B 497 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.7533 (t80) REVERT: B 568 TRP cc_start: 0.8345 (OUTLIER) cc_final: 0.5448 (t60) REVERT: B 681 HIS cc_start: 0.7796 (OUTLIER) cc_final: 0.7538 (m-70) REVERT: U 226 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8069 (mtt90) REVERT: U 417 TYR cc_start: 0.5496 (OUTLIER) cc_final: 0.4716 (m-80) REVERT: V 177 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8674 (tp) REVERT: V 226 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.7642 (mtp180) REVERT: V 291 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8615 (pt) REVERT: V 370 ARG cc_start: 0.6681 (ttp80) cc_final: 0.6459 (ttp80) REVERT: V 380 MET cc_start: 0.7252 (ppp) cc_final: 0.6882 (ppp) REVERT: V 598 GLN cc_start: 0.4638 (OUTLIER) cc_final: 0.4112 (pt0) outliers start: 153 outliers final: 104 residues processed: 379 average time/residue: 0.4079 time to fit residues: 265.6422 Evaluate side-chains 348 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 230 time to evaluate : 3.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain U residue 40 GLU Chi-restraints excluded: chain U residue 41 GLU Chi-restraints excluded: chain U residue 62 ASN Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 146 LEU Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 191 MET Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 236 SER Chi-restraints excluded: chain U residue 238 PHE Chi-restraints excluded: chain U residue 268 VAL Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 291 LEU Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 312 GLN Chi-restraints excluded: chain U residue 343 VAL Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 417 TYR Chi-restraints excluded: chain U residue 466 TYR Chi-restraints excluded: chain U residue 527 VAL Chi-restraints excluded: chain U residue 543 LEU Chi-restraints excluded: chain U residue 559 THR Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 163 LEU Chi-restraints excluded: chain V residue 176 THR Chi-restraints excluded: chain V residue 177 LEU 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 220 ILE Chi-restraints excluded: chain V residue 226 ARG Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 273 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 334 THR 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 438 LEU Chi-restraints excluded: chain V residue 442 ILE Chi-restraints excluded: chain V residue 502 SER Chi-restraints excluded: chain V residue 536 GLU Chi-restraints excluded: chain V residue 576 VAL Chi-restraints excluded: chain V residue 598 GLN Chi-restraints excluded: chain V residue 612 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 499 optimal weight: 50.0000 chunk 455 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 463 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 401 optimal weight: 9.9990 chunk 476 optimal weight: 30.0000 chunk 446 optimal weight: 10.0000 chunk 511 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 315 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS B 595 HIS B 676 ASN B 681 HIS ** B 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.178617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.157026 restraints weight = 71574.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.153568 restraints weight = 91376.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.149928 restraints weight = 89580.341| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 34745 Z= 0.283 Angle : 0.684 13.509 47662 Z= 0.348 Chirality : 0.048 0.313 5593 Planarity : 0.005 0.078 6453 Dihedral : 8.317 101.379 5806 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.92 % Favored : 90.98 % Rotamer: Outliers : 7.25 % Allowed : 26.36 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.10 (0.12), residues: 5156 helix: 1.61 (0.14), residues: 1496 sheet: -1.76 (0.19), residues: 852 loop : -1.77 (0.11), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP U 462 HIS 0.015 0.001 HIS U 256 PHE 0.025 0.002 PHE B 428 TYR 0.023 0.002 TYR B 438 ARG 0.015 0.001 ARG V 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 5) link_NAG-ASN : angle 2.36950 ( 15) link_BETA1-4 : bond 0.00300 ( 2) link_BETA1-4 : angle 2.25338 ( 6) hydrogen bonds : bond 0.03633 ( 1205) hydrogen bonds : angle 4.42665 ( 3417) SS BOND : bond 0.01192 ( 8) SS BOND : angle 2.70997 ( 16) covalent geometry : bond 0.00683 (34730) covalent geometry : angle 0.68045 (47625) *********************** 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 394 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 229 time to evaluate : 3.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: A 729 ARG cc_start: 0.5085 (OUTLIER) cc_final: 0.4694 (ptm160) REVERT: B 73 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.5786 (mt-10) REVERT: B 234 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8200 (m-30) REVERT: B 281 PHE cc_start: 0.7927 (t80) cc_final: 0.7708 (t80) REVERT: B 323 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.5411 (m-80) REVERT: B 497 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.7603 (t80) REVERT: B 568 TRP cc_start: 0.8406 (OUTLIER) cc_final: 0.5613 (t60) REVERT: U 259 TYR cc_start: 0.8405 (t80) cc_final: 0.8160 (t80) REVERT: U 309 MET cc_start: 0.7170 (mtt) cc_final: 0.6935 (mtm) REVERT: U 417 TYR cc_start: 0.5488 (OUTLIER) cc_final: 0.4724 (m-80) REVERT: U 518 MET cc_start: 0.1764 (mmp) cc_final: 0.0776 (mmp) REVERT: U 561 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.6309 (m-80) REVERT: V 41 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7906 (pt0) REVERT: V 177 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8843 (tp) REVERT: V 291 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8333 (pt) REVERT: V 370 ARG cc_start: 0.6694 (ttp80) cc_final: 0.6447 (ttp80) REVERT: V 380 MET cc_start: 0.7377 (ppp) cc_final: 0.6959 (ppp) REVERT: V 598 GLN cc_start: 0.4840 (OUTLIER) cc_final: 0.4404 (pt0) outliers start: 165 outliers final: 122 residues processed: 382 average time/residue: 0.4145 time to fit residues: 272.1487 Evaluate side-chains 364 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 229 time to evaluate : 3.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain U residue 40 GLU Chi-restraints excluded: chain U residue 41 GLU Chi-restraints excluded: chain U residue 55 LEU Chi-restraints excluded: chain U residue 62 ASN Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 146 LEU Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 191 MET Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 236 SER Chi-restraints excluded: chain U residue 237 THR Chi-restraints excluded: chain U residue 238 PHE Chi-restraints excluded: chain U residue 268 VAL Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 291 LEU Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 307 SER Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 312 GLN Chi-restraints excluded: chain U residue 343 VAL Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 417 TYR Chi-restraints excluded: chain U residue 522 ASP Chi-restraints excluded: chain U residue 527 VAL Chi-restraints excluded: chain U residue 550 SER Chi-restraints excluded: chain U residue 559 THR Chi-restraints excluded: chain U residue 561 TYR Chi-restraints excluded: chain U residue 614 LEU Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 163 LEU Chi-restraints excluded: chain V residue 176 THR Chi-restraints excluded: chain V residue 177 LEU 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 220 ILE Chi-restraints excluded: chain V residue 239 LEU Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 273 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 334 THR 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 438 LEU Chi-restraints excluded: chain V residue 442 ILE Chi-restraints excluded: chain V residue 463 ASP Chi-restraints excluded: chain V residue 502 SER Chi-restraints excluded: chain V residue 536 GLU Chi-restraints excluded: chain V residue 576 VAL Chi-restraints excluded: chain V residue 598 GLN Chi-restraints excluded: chain V residue 612 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 196 optimal weight: 50.0000 chunk 72 optimal weight: 0.8980 chunk 367 optimal weight: 0.8980 chunk 222 optimal weight: 50.0000 chunk 8 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 449 optimal weight: 30.0000 chunk 183 optimal weight: 30.0000 chunk 157 optimal weight: 50.0000 chunk 22 optimal weight: 1.9990 chunk 214 optimal weight: 50.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS B 478 GLN B 595 HIS B 681 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.180762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.157772 restraints weight = 70013.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.154970 restraints weight = 92312.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.151396 restraints weight = 87280.269| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 34745 Z= 0.200 Angle : 0.626 13.274 47662 Z= 0.315 Chirality : 0.046 0.295 5593 Planarity : 0.004 0.077 6453 Dihedral : 7.867 95.712 5802 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.43 % Favored : 92.47 % Rotamer: Outliers : 6.63 % Allowed : 26.80 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.96 (0.12), residues: 5156 helix: 1.73 (0.14), residues: 1492 sheet: -1.67 (0.19), residues: 804 loop : -1.69 (0.11), residues: 2860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP U 462 HIS 0.015 0.001 HIS U 256 PHE 0.018 0.002 PHE U 238 TYR 0.026 0.002 TYR B 438 ARG 0.008 0.000 ARG V 360 Details of bonding type rmsd link_NAG-ASN : bond 0.00308 ( 5) link_NAG-ASN : angle 2.24884 ( 15) link_BETA1-4 : bond 0.00447 ( 2) link_BETA1-4 : angle 2.02008 ( 6) hydrogen bonds : bond 0.03235 ( 1205) hydrogen bonds : angle 4.27222 ( 3417) SS BOND : bond 0.01121 ( 8) SS BOND : angle 2.33770 ( 16) covalent geometry : bond 0.00480 (34730) covalent geometry : angle 0.62296 (47625) *********************** 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 386 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 235 time to evaluate : 3.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: A 729 ARG cc_start: 0.5039 (OUTLIER) cc_final: 0.4712 (ptm160) REVERT: B 73 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.5702 (mt-10) REVERT: B 234 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8286 (m-30) REVERT: B 281 PHE cc_start: 0.7769 (t80) cc_final: 0.7521 (t80) REVERT: B 323 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.5328 (m-80) REVERT: B 497 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.7558 (t80) REVERT: B 568 TRP cc_start: 0.8393 (OUTLIER) cc_final: 0.5790 (t60) REVERT: B 681 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.7217 (m-70) REVERT: U 226 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8017 (mtt90) REVERT: U 259 TYR cc_start: 0.8342 (t80) cc_final: 0.8094 (t80) REVERT: U 309 MET cc_start: 0.7171 (mtt) cc_final: 0.6920 (mtm) REVERT: U 417 TYR cc_start: 0.5458 (OUTLIER) cc_final: 0.4626 (m-80) REVERT: U 561 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.6411 (m-80) REVERT: V 177 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8486 (tp) REVERT: V 291 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8686 (pt) REVERT: V 380 MET cc_start: 0.7391 (ppp) cc_final: 0.6962 (ppp) REVERT: V 598 GLN cc_start: 0.4724 (OUTLIER) cc_final: 0.4325 (pt0) outliers start: 151 outliers final: 120 residues processed: 374 average time/residue: 0.4099 time to fit residues: 265.1154 Evaluate side-chains 361 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 227 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain U residue 40 GLU Chi-restraints excluded: chain U residue 41 GLU Chi-restraints excluded: chain U residue 62 ASN Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 146 LEU Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 191 MET Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 236 SER Chi-restraints excluded: chain U residue 237 THR Chi-restraints excluded: chain U residue 238 PHE Chi-restraints excluded: chain U residue 268 VAL Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 291 LEU Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 307 SER Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 312 GLN Chi-restraints excluded: chain U residue 343 VAL Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 417 TYR Chi-restraints excluded: chain U residue 463 ASP Chi-restraints excluded: chain U residue 527 VAL Chi-restraints excluded: chain U residue 550 SER Chi-restraints excluded: chain U residue 559 THR Chi-restraints excluded: chain U residue 561 TYR Chi-restraints excluded: chain U residue 614 LEU Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 79 HIS Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 163 LEU Chi-restraints excluded: chain V residue 176 THR Chi-restraints excluded: chain V residue 177 LEU 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 220 ILE Chi-restraints excluded: chain V residue 241 ASP 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 334 THR 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 424 VAL Chi-restraints excluded: chain V residue 438 LEU Chi-restraints excluded: chain V residue 442 ILE Chi-restraints excluded: chain V residue 502 SER Chi-restraints excluded: chain V residue 536 GLU Chi-restraints excluded: chain V residue 576 VAL Chi-restraints excluded: chain V residue 598 GLN Chi-restraints excluded: chain V residue 612 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 301 optimal weight: 0.7980 chunk 236 optimal weight: 50.0000 chunk 384 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 391 optimal weight: 9.9990 chunk 499 optimal weight: 8.9990 chunk 442 optimal weight: 50.0000 chunk 123 optimal weight: 0.0030 chunk 397 optimal weight: 9.9990 chunk 464 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 overall best weight: 2.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 ASN ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS B 595 HIS B 676 ASN B 681 HIS ** B 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.188015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.166194 restraints weight = 71750.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.163867 restraints weight = 91466.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.160554 restraints weight = 80091.895| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 34745 Z= 0.253 Angle : 0.673 16.531 47662 Z= 0.339 Chirality : 0.047 0.316 5593 Planarity : 0.005 0.076 6453 Dihedral : 8.027 99.699 5802 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.00 % Favored : 90.90 % Rotamer: Outliers : 6.72 % Allowed : 26.76 % Favored : 66.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.05 (0.12), residues: 5156 helix: 1.66 (0.14), residues: 1488 sheet: -1.73 (0.19), residues: 848 loop : -1.73 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP U 462 HIS 0.018 0.001 HIS B 681 PHE 0.022 0.002 PHE B 428 TYR 0.023 0.002 TYR B 438 ARG 0.006 0.000 ARG A 287 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 5) link_NAG-ASN : angle 2.25733 ( 15) link_BETA1-4 : bond 0.00318 ( 2) link_BETA1-4 : angle 2.18652 ( 6) hydrogen bonds : bond 0.03490 ( 1205) hydrogen bonds : angle 4.34663 ( 3417) SS BOND : bond 0.01190 ( 8) SS BOND : angle 2.53462 ( 16) covalent geometry : bond 0.00609 (34730) covalent geometry : angle 0.66967 (47625) *********************** 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 388 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 235 time to evaluate : 3.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.5608 (mt-10) REVERT: A 574 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: B 73 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.5758 (mt-10) REVERT: B 79 ASP cc_start: 0.4364 (OUTLIER) cc_final: 0.4159 (p0) REVERT: B 234 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8226 (m-30) REVERT: B 281 PHE cc_start: 0.7709 (t80) cc_final: 0.7474 (t80) REVERT: B 323 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.5435 (m-80) REVERT: B 497 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.7562 (t80) REVERT: B 568 TRP cc_start: 0.8409 (OUTLIER) cc_final: 0.5773 (t60) REVERT: U 309 MET cc_start: 0.7142 (mtt) cc_final: 0.6890 (mtm) REVERT: U 413 PHE cc_start: 0.6274 (t80) cc_final: 0.5565 (t80) REVERT: U 417 TYR cc_start: 0.5490 (OUTLIER) cc_final: 0.4640 (m-80) REVERT: U 518 MET cc_start: 0.1513 (mmp) cc_final: 0.0271 (mmp) REVERT: U 561 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.6356 (m-80) REVERT: V 177 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8815 (tp) REVERT: V 291 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8556 (pt) REVERT: V 370 ARG cc_start: 0.6666 (ttp80) cc_final: 0.6408 (ttp80) REVERT: V 380 MET cc_start: 0.7390 (ppp) cc_final: 0.6995 (ppp) REVERT: V 598 GLN cc_start: 0.4746 (OUTLIER) cc_final: 0.4338 (pt0) outliers start: 153 outliers final: 126 residues processed: 378 average time/residue: 0.4093 time to fit residues: 267.8228 Evaluate side-chains 370 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 231 time to evaluate : 3.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain U residue 40 GLU Chi-restraints excluded: chain U residue 41 GLU Chi-restraints excluded: chain U residue 62 ASN Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 146 LEU Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 191 MET Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 236 SER Chi-restraints excluded: chain U residue 237 THR Chi-restraints excluded: chain U residue 238 PHE Chi-restraints excluded: chain U residue 268 VAL Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 291 LEU Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 307 SER Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 312 GLN Chi-restraints excluded: chain U residue 343 VAL Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 417 TYR Chi-restraints excluded: chain U residue 463 ASP Chi-restraints excluded: chain U residue 522 ASP Chi-restraints excluded: chain U residue 527 VAL Chi-restraints excluded: chain U residue 550 SER Chi-restraints excluded: chain U residue 559 THR Chi-restraints excluded: chain U residue 561 TYR Chi-restraints excluded: chain U residue 614 LEU Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 79 HIS Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 163 LEU Chi-restraints excluded: chain V residue 176 THR Chi-restraints excluded: chain V residue 177 LEU 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 220 ILE Chi-restraints excluded: chain V residue 239 LEU Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 273 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 334 THR 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 424 VAL Chi-restraints excluded: chain V residue 438 LEU Chi-restraints excluded: chain V residue 442 ILE Chi-restraints excluded: chain V residue 502 SER Chi-restraints excluded: chain V residue 536 GLU Chi-restraints excluded: chain V residue 576 VAL Chi-restraints excluded: chain V residue 598 GLN Chi-restraints excluded: chain V residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 231 optimal weight: 6.9990 chunk 159 optimal weight: 40.0000 chunk 135 optimal weight: 0.7980 chunk 339 optimal weight: 0.8980 chunk 78 optimal weight: 0.0970 chunk 509 optimal weight: 40.0000 chunk 351 optimal weight: 0.0980 chunk 466 optimal weight: 0.8980 chunk 108 optimal weight: 0.4980 chunk 227 optimal weight: 9.9990 chunk 188 optimal weight: 30.0000 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS B 595 HIS B 676 ASN ** B 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.188220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.166260 restraints weight = 71295.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.163200 restraints weight = 92742.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.159633 restraints weight = 90791.255| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.193 34745 Z= 0.214 Angle : 0.828 59.200 47662 Z= 0.456 Chirality : 0.047 0.550 5593 Planarity : 0.005 0.077 6453 Dihedral : 8.025 99.607 5802 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.88 % Favored : 91.02 % Rotamer: Outliers : 6.41 % Allowed : 27.20 % Favored : 66.39 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.03 (0.12), residues: 5156 helix: 1.68 (0.14), residues: 1488 sheet: -1.74 (0.19), residues: 848 loop : -1.72 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP U 462 HIS 0.018 0.001 HIS B 681 PHE 0.021 0.002 PHE U 238 TYR 0.021 0.002 TYR V 198 ARG 0.005 0.000 ARG V 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 5) link_NAG-ASN : angle 2.25515 ( 15) link_BETA1-4 : bond 0.00278 ( 2) link_BETA1-4 : angle 2.13739 ( 6) hydrogen bonds : bond 0.03360 ( 1205) hydrogen bonds : angle 4.33830 ( 3417) SS BOND : bond 0.01106 ( 8) SS BOND : angle 2.67643 ( 16) covalent geometry : bond 0.00497 (34730) covalent geometry : angle 0.82591 (47625) ********************** 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 377 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 231 time to evaluate : 3.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.5598 (mt-10) REVERT: A 574 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: A 651 ASN cc_start: 0.7884 (OUTLIER) cc_final: 0.7589 (p0) REVERT: B 73 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.5752 (mt-10) REVERT: B 234 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8216 (m-30) REVERT: B 281 PHE cc_start: 0.7727 (t80) cc_final: 0.7502 (t80) REVERT: B 323 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.5413 (m-80) REVERT: B 497 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.7612 (t80) REVERT: B 568 TRP cc_start: 0.8369 (OUTLIER) cc_final: 0.5714 (t60) REVERT: B 676 ASN cc_start: 0.8608 (OUTLIER) cc_final: 0.8130 (t0) REVERT: U 309 MET cc_start: 0.7147 (mtt) cc_final: 0.6895 (mtm) REVERT: U 340 PHE cc_start: 0.6965 (OUTLIER) cc_final: 0.6309 (m-10) REVERT: U 413 PHE cc_start: 0.6314 (t80) cc_final: 0.5593 (t80) REVERT: U 417 TYR cc_start: 0.5526 (OUTLIER) cc_final: 0.4652 (m-80) REVERT: U 518 MET cc_start: 0.1616 (mmp) cc_final: 0.0401 (mmp) REVERT: U 561 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.6382 (m-80) REVERT: V 177 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8751 (tp) REVERT: V 291 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8588 (pt) REVERT: V 370 ARG cc_start: 0.6661 (ttp80) cc_final: 0.6393 (ttp80) REVERT: V 380 MET cc_start: 0.7407 (ppp) cc_final: 0.6997 (ppp) REVERT: V 598 GLN cc_start: 0.4777 (OUTLIER) cc_final: 0.4368 (pt0) outliers start: 146 outliers final: 127 residues processed: 366 average time/residue: 0.4051 time to fit residues: 256.5515 Evaluate side-chains 369 residues out of total 4552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 227 time to evaluate : 3.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 282 CYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 574 GLU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 700 ILE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 79 ASP Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 323 TYR Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 MET Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 514 ARG Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 568 TRP Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 676 ASN Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 722 LEU Chi-restraints excluded: chain B residue 731 ILE Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain U residue 40 GLU Chi-restraints excluded: chain U residue 41 GLU Chi-restraints excluded: chain U residue 62 ASN Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 146 LEU Chi-restraints excluded: chain U residue 160 ASP Chi-restraints excluded: chain U residue 191 MET Chi-restraints excluded: chain U residue 203 CYS Chi-restraints excluded: chain U residue 226 ARG Chi-restraints excluded: chain U residue 236 SER Chi-restraints excluded: chain U residue 237 THR Chi-restraints excluded: chain U residue 238 PHE Chi-restraints excluded: chain U residue 268 VAL Chi-restraints excluded: chain U residue 273 CYS Chi-restraints excluded: chain U residue 291 LEU Chi-restraints excluded: chain U residue 293 VAL Chi-restraints excluded: chain U residue 300 THR Chi-restraints excluded: chain U residue 307 SER Chi-restraints excluded: chain U residue 311 VAL Chi-restraints excluded: chain U residue 312 GLN Chi-restraints excluded: chain U residue 340 PHE Chi-restraints excluded: chain U residue 343 VAL Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain U residue 417 TYR Chi-restraints excluded: chain U residue 438 LEU Chi-restraints excluded: chain U residue 463 ASP Chi-restraints excluded: chain U residue 522 ASP Chi-restraints excluded: chain U residue 527 VAL Chi-restraints excluded: chain U residue 550 SER Chi-restraints excluded: chain U residue 559 THR Chi-restraints excluded: chain U residue 561 TYR Chi-restraints excluded: chain U residue 614 LEU Chi-restraints excluded: chain V residue 47 SER Chi-restraints excluded: chain V residue 79 HIS Chi-restraints excluded: chain V residue 108 VAL Chi-restraints excluded: chain V residue 143 VAL Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 163 LEU Chi-restraints excluded: chain V residue 176 THR Chi-restraints excluded: chain V residue 177 LEU 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 220 ILE Chi-restraints excluded: chain V residue 239 LEU Chi-restraints excluded: chain V residue 241 ASP Chi-restraints excluded: chain V residue 273 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 334 THR 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 424 VAL Chi-restraints excluded: chain V residue 428 LEU Chi-restraints excluded: chain V residue 438 LEU Chi-restraints excluded: chain V residue 442 ILE Chi-restraints excluded: chain V residue 502 SER Chi-restraints excluded: chain V residue 536 GLU Chi-restraints excluded: chain V residue 576 VAL Chi-restraints excluded: chain V residue 598 GLN Chi-restraints excluded: chain V residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 512 random chunks: chunk 265 optimal weight: 50.0000 chunk 461 optimal weight: 40.0000 chunk 31 optimal weight: 1.9990 chunk 323 optimal weight: 0.0030 chunk 368 optimal weight: 4.9990 chunk 459 optimal weight: 50.0000 chunk 224 optimal weight: 20.0000 chunk 345 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 154 optimal weight: 50.0000 chunk 250 optimal weight: 8.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 HIS B 595 HIS B 676 ASN ** B 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 717 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.188362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.165688 restraints weight = 71623.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.162873 restraints weight = 94861.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.159590 restraints weight = 88994.899| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 1.068 34745 Z= 0.358 Angle : 0.794 57.543 47662 Z= 0.435 Chirality : 0.047 0.550 5593 Planarity : 0.005 0.086 6453 Dihedral : 8.025 99.607 5802 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.88 % Favored : 91.02 % Rotamer: Outliers : 6.20 % Allowed : 27.42 % Favored : 66.39 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.03 (0.12), residues: 5156 helix: 1.68 (0.14), residues: 1488 sheet: -1.74 (0.19), residues: 848 loop : -1.72 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP U 462 HIS 0.018 0.001 HIS B 681 PHE 0.021 0.002 PHE U 238 TYR 0.021 0.002 TYR V 198 ARG 0.005 0.000 ARG V 544 Details of bonding type rmsd link_NAG-ASN : bond 0.00285 ( 5) link_NAG-ASN : angle 2.25515 ( 15) link_BETA1-4 : bond 0.00278 ( 2) link_BETA1-4 : angle 2.13739 ( 6) hydrogen bonds : bond 0.03360 ( 1205) hydrogen bonds : angle 4.33830 ( 3417) SS BOND : bond 0.37775 ( 8) SS BOND : angle 8.78190 ( 16) covalent geometry : bond 0.00496 (34730) covalent geometry : angle 0.77674 (47625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11443.49 seconds wall clock time: 201 minutes 4.67 seconds (12064.67 seconds total)