Starting phenix.real_space_refine on Mon Apr 8 18:16:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm6_20389/04_2024/6pm6_20389.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm6_20389/04_2024/6pm6_20389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm6_20389/04_2024/6pm6_20389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm6_20389/04_2024/6pm6_20389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm6_20389/04_2024/6pm6_20389.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm6_20389/04_2024/6pm6_20389.pdb" } resolution = 2.9 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= 0.060 sd= 3.254 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9185 2.51 5 N 2260 2.21 5 O 2555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 407": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14100 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 7.59, per 1000 atoms: 0.54 Number of scatterers: 14100 At special positions: 0 Unit cell: (106.167, 102.875, 134.972, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2555 8.00 N 2260 7.00 C 9185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN D 54 " " NAG H 1 " - " ASN B 54 " " NAG I 1 " - " ASN C 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 5.17 Conformation dependent library (CDL) restraints added in 2.3 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 25 sheets defined 38.6% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.523A pdb=" N PHE A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.972A pdb=" N GLY A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR A 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 36 through 40' Processing helix chain 'A' and resid 87 through 90 removed outlier: 3.522A pdb=" N ALA A 90 " --> pdb=" O PRO A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.951A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 248 through 257 removed outlier: 3.518A pdb=" N ILE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 286 removed outlier: 3.575A pdb=" N GLY A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 283 " --> pdb=" O MET A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 304 through 325 removed outlier: 3.550A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 removed outlier: 3.577A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 427 removed outlier: 4.010A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 35 removed outlier: 3.541A pdb=" N PHE D 29 " --> pdb=" O PRO D 25 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 30 " --> pdb=" O PRO D 26 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 removed outlier: 4.014A pdb=" N GLY D 39 " --> pdb=" O LYS D 36 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR D 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 36 through 40' Processing helix chain 'D' and resid 87 through 90 removed outlier: 3.556A pdb=" N ALA D 90 " --> pdb=" O PRO D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 104 through 108 removed outlier: 4.024A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 163 Processing helix chain 'D' and resid 236 through 243 removed outlier: 3.800A pdb=" N ILE D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 247 Processing helix chain 'D' and resid 248 through 257 removed outlier: 3.550A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 286 removed outlier: 3.558A pdb=" N GLY D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 277 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER D 283 " --> pdb=" O MET D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 304 through 325 removed outlier: 3.551A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 406 removed outlier: 4.396A pdb=" N LEU D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA D 399 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE D 402 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 427 removed outlier: 4.009A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.544A pdb=" N PHE B 29 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 30 " --> pdb=" O PRO B 26 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASP B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.904A pdb=" N GLY B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR B 40 " --> pdb=" O VAL B 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 40' Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 104 through 108 removed outlier: 4.056A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 163 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 248 through 257 removed outlier: 3.530A pdb=" N ILE B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 286 removed outlier: 3.544A pdb=" N GLY B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 277 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 283 " --> pdb=" O MET B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 304 through 325 removed outlier: 3.637A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.552A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 427 removed outlier: 4.020A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.577A pdb=" N PHE C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 40 removed outlier: 3.980A pdb=" N GLY C 39 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR C 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 36 through 40' Processing helix chain 'C' and resid 87 through 90 removed outlier: 3.503A pdb=" N ALA C 90 " --> pdb=" O PRO C 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 90' Processing helix chain 'C' and resid 104 through 108 removed outlier: 4.017A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 163 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 244 through 247 Processing helix chain 'C' and resid 248 through 257 removed outlier: 3.537A pdb=" N ILE C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 286 removed outlier: 3.538A pdb=" N GLY C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 277 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 283 " --> pdb=" O MET C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 304 through 325 removed outlier: 3.575A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 406 removed outlier: 3.561A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 427 removed outlier: 3.942A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.567A pdb=" N PHE E 29 " --> pdb=" O PRO E 25 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 30 " --> pdb=" O PRO E 26 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 40 removed outlier: 3.964A pdb=" N GLY E 39 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR E 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 36 through 40' Processing helix chain 'E' and resid 87 through 90 removed outlier: 3.531A pdb=" N ALA E 90 " --> pdb=" O PRO E 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 90' Processing helix chain 'E' and resid 104 through 108 removed outlier: 3.980A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 163 Processing helix chain 'E' and resid 238 through 243 Processing helix chain 'E' and resid 244 through 247 Processing helix chain 'E' and resid 248 through 257 removed outlier: 3.538A pdb=" N ILE E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 286 removed outlier: 4.224A pdb=" N VAL E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY E 272 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E 277 " --> pdb=" O ILE E 273 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER E 283 " --> pdb=" O MET E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 304 through 325 removed outlier: 3.567A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 406 removed outlier: 3.554A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA E 399 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE E 402 " --> pdb=" O ARG E 398 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 427 removed outlier: 3.964A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.556A pdb=" N ILE A 136 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 6.497A pdb=" N ASP A 73 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER A 66 " --> pdb=" O ASP A 73 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N GLN A 193 " --> pdb=" O CYS A 57 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 116 Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA6, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.630A pdb=" N ILE D 136 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.366A pdb=" N ASP D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER D 66 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N GLN D 193 " --> pdb=" O CYS D 57 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AB1, first strand: chain 'D' and resid 216 through 217 Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.555A pdb=" N ILE B 136 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.419A pdb=" N ASP B 73 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER B 66 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N GLN B 193 " --> pdb=" O CYS B 57 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB5, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AB6, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AB7, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.582A pdb=" N ILE C 136 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.444A pdb=" N ASP C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N SER C 66 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N GLN C 193 " --> pdb=" O CYS C 57 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AC1, first strand: chain 'C' and resid 114 through 116 Processing sheet with id=AC2, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AC3, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.587A pdb=" N ILE E 136 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.416A pdb=" N ASP E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER E 66 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N GLN E 193 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC6, first strand: chain 'E' and resid 114 through 116 Processing sheet with id=AC7, first strand: chain 'E' and resid 216 through 217 677 hydrogen bonds defined for protein. 1968 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: 4.57 Time building geometry restraints manager: 5.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4313 1.34 - 1.47: 3630 1.47 - 1.59: 6332 1.59 - 1.71: 0 1.71 - 1.83: 170 Bond restraints: 14445 Sorted by residual: bond pdb=" C PHE D 410 " pdb=" N PRO D 411 " ideal model delta sigma weight residual 1.334 1.368 -0.035 8.40e-03 1.42e+04 1.71e+01 bond pdb=" C PHE A 410 " pdb=" N PRO A 411 " ideal model delta sigma weight residual 1.334 1.368 -0.035 8.40e-03 1.42e+04 1.70e+01 bond pdb=" C PHE E 410 " pdb=" N PRO E 411 " ideal model delta sigma weight residual 1.334 1.368 -0.034 8.40e-03 1.42e+04 1.69e+01 bond pdb=" C PHE C 410 " pdb=" N PRO C 411 " ideal model delta sigma weight residual 1.334 1.368 -0.034 8.40e-03 1.42e+04 1.67e+01 bond pdb=" C PHE B 410 " pdb=" N PRO B 411 " ideal model delta sigma weight residual 1.334 1.367 -0.034 8.40e-03 1.42e+04 1.61e+01 ... (remaining 14440 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.72: 511 106.72 - 113.56: 7809 113.56 - 120.39: 5497 120.39 - 127.23: 5617 127.23 - 134.07: 176 Bond angle restraints: 19610 Sorted by residual: angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 131.89 -10.35 1.91e+00 2.74e-01 2.94e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 131.83 -10.29 1.91e+00 2.74e-01 2.90e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 131.74 -10.20 1.91e+00 2.74e-01 2.85e+01 angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 131.68 -10.14 1.91e+00 2.74e-01 2.82e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 131.66 -10.12 1.91e+00 2.74e-01 2.81e+01 ... (remaining 19605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 8347 16.01 - 32.02: 339 32.02 - 48.03: 51 48.03 - 64.05: 45 64.05 - 80.06: 33 Dihedral angle restraints: 8815 sinusoidal: 3700 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 50.76 42.24 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 51.08 41.92 1 1.00e+01 1.00e-02 2.46e+01 dihedral pdb=" CB CYS B 154 " pdb=" SG CYS B 154 " pdb=" SG CYS B 168 " pdb=" CB CYS B 168 " ideal model delta sinusoidal sigma weight residual 93.00 51.12 41.88 1 1.00e+01 1.00e-02 2.45e+01 ... (remaining 8812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1553 0.051 - 0.101: 538 0.101 - 0.152: 139 0.152 - 0.202: 15 0.202 - 0.253: 15 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 2.03e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 2257 not shown) Planarity restraints: 2435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 410 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO B 411 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 411 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 411 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 410 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.16e+00 pdb=" N PRO D 411 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 411 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 411 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 410 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO A 411 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " 0.042 5.00e-02 4.00e+02 ... (remaining 2432 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4537 2.85 - 3.36: 12059 3.36 - 3.87: 22417 3.87 - 4.39: 26556 4.39 - 4.90: 44747 Nonbonded interactions: 110316 Sorted by model distance: nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.335 2.440 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.336 2.440 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.342 2.440 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.344 2.440 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.346 2.440 ... (remaining 110311 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.010 Extract box with map and model: 7.240 Check model and map are aligned: 0.190 Set scattering table: 0.140 Process input model: 38.580 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.130 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:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 0.046 14445 Z= 0.299 Angle : 0.922 10.349 19610 Z= 0.481 Chirality : 0.055 0.253 2260 Planarity : 0.007 0.076 2430 Dihedral : 11.654 80.057 5465 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.86 (0.15), residues: 1710 helix: -4.79 (0.07), residues: 550 sheet: -1.89 (0.23), residues: 385 loop : -2.57 (0.18), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 110 HIS 0.002 0.001 HIS C 125 PHE 0.021 0.002 PHE A 115 TYR 0.017 0.002 TYR D 425 ARG 0.008 0.001 ARG B 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 1.491 Fit side-chains REVERT: A 75 ARG cc_start: 0.7302 (ttm-80) cc_final: 0.6919 (ttm110) REVERT: A 206 LYS cc_start: 0.8301 (mtpt) cc_final: 0.8047 (mttt) REVERT: A 210 ASP cc_start: 0.8048 (m-30) cc_final: 0.7306 (t0) REVERT: A 222 LYS cc_start: 0.7945 (ptmm) cc_final: 0.7579 (pttt) REVERT: A 292 LYS cc_start: 0.8062 (mttt) cc_final: 0.7690 (mttp) REVERT: A 391 MET cc_start: 0.6841 (mtp) cc_final: 0.6363 (tmm) REVERT: A 419 ILE cc_start: 0.8385 (mt) cc_final: 0.8131 (mp) REVERT: D 32 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7965 (tmtt) REVERT: D 75 ARG cc_start: 0.7453 (ttm-80) cc_final: 0.7024 (ttm110) REVERT: D 206 LYS cc_start: 0.8259 (mtpt) cc_final: 0.8012 (mtmm) REVERT: D 210 ASP cc_start: 0.7951 (m-30) cc_final: 0.7046 (t0) REVERT: D 222 LYS cc_start: 0.7879 (ptmm) cc_final: 0.7490 (pttt) REVERT: D 292 LYS cc_start: 0.8120 (mttt) cc_final: 0.7861 (mttp) REVERT: D 391 MET cc_start: 0.6743 (mtp) cc_final: 0.5594 (tpt) REVERT: D 420 PHE cc_start: 0.7334 (t80) cc_final: 0.7096 (t80) REVERT: B 32 LYS cc_start: 0.8286 (ttpt) cc_final: 0.8034 (tmtt) REVERT: B 210 ASP cc_start: 0.7886 (m-30) cc_final: 0.7079 (t0) REVERT: B 222 LYS cc_start: 0.7893 (ptmm) cc_final: 0.7573 (pttt) REVERT: B 279 MET cc_start: 0.8169 (mmm) cc_final: 0.7597 (mmt) REVERT: B 292 LYS cc_start: 0.8105 (mttt) cc_final: 0.7756 (mttp) REVERT: B 401 ARG cc_start: 0.5233 (tpt170) cc_final: 0.4987 (tmt90) REVERT: C 28 GLU cc_start: 0.7625 (tp30) cc_final: 0.7023 (tp30) REVERT: C 32 LYS cc_start: 0.8392 (ttpt) cc_final: 0.8095 (tttp) REVERT: C 75 ARG cc_start: 0.7381 (ttm-80) cc_final: 0.7149 (mtp-110) REVERT: C 206 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7896 (mtmm) REVERT: C 210 ASP cc_start: 0.7846 (m-30) cc_final: 0.7070 (t0) REVERT: C 222 LYS cc_start: 0.7777 (ptmm) cc_final: 0.7488 (pttt) REVERT: C 420 PHE cc_start: 0.7290 (t80) cc_final: 0.7039 (t80) REVERT: E 32 LYS cc_start: 0.8286 (ttpt) cc_final: 0.8044 (tmtt) REVERT: E 75 ARG cc_start: 0.7486 (ttm-80) cc_final: 0.7128 (ttm110) REVERT: E 206 LYS cc_start: 0.8311 (mtpt) cc_final: 0.8100 (mtmm) REVERT: E 210 ASP cc_start: 0.7856 (m-30) cc_final: 0.7050 (t0) REVERT: E 391 MET cc_start: 0.6643 (mtp) cc_final: 0.6382 (ttp) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 1.0736 time to fit residues: 479.9481 Evaluate side-chains 285 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.0770 chunk 68 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 81 optimal weight: 0.0470 chunk 99 optimal weight: 0.9990 chunk 154 optimal weight: 4.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN D 77 ASN D 219 ASN D 231 HIS B 77 ASN B 141 ASN B 231 HIS C 77 ASN C 219 ASN C 231 HIS E 77 ASN E 219 ASN E 231 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14445 Z= 0.214 Angle : 0.745 13.583 19610 Z= 0.378 Chirality : 0.049 0.324 2260 Planarity : 0.005 0.050 2430 Dihedral : 10.049 59.526 2185 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.90 % Allowed : 11.62 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.57 (0.17), residues: 1710 helix: -3.03 (0.16), residues: 565 sheet: -1.09 (0.26), residues: 385 loop : -2.42 (0.18), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 84 HIS 0.004 0.001 HIS B 231 PHE 0.013 0.001 PHE D 309 TYR 0.012 0.002 TYR A 317 ARG 0.007 0.001 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 316 time to evaluate : 1.574 Fit side-chains REVERT: A 49 LYS cc_start: 0.8780 (mttt) cc_final: 0.8252 (mtpt) REVERT: A 69 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: A 75 ARG cc_start: 0.7399 (ttm-80) cc_final: 0.6951 (ttm110) REVERT: A 96 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7410 (t0) REVERT: A 97 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7442 (t0) REVERT: A 179 MET cc_start: 0.8498 (mmm) cc_final: 0.7972 (tpt) REVERT: A 206 LYS cc_start: 0.8304 (mtpt) cc_final: 0.8063 (mttt) REVERT: A 212 ARG cc_start: 0.7626 (ptp-110) cc_final: 0.7348 (ptp-110) REVERT: A 292 LYS cc_start: 0.8147 (mttt) cc_final: 0.7781 (mttp) REVERT: A 303 MET cc_start: 0.8810 (mmm) cc_final: 0.8508 (mmt) REVERT: A 391 MET cc_start: 0.6640 (mtp) cc_final: 0.6406 (tmm) REVERT: A 420 PHE cc_start: 0.7577 (t80) cc_final: 0.6791 (t80) REVERT: D 62 ASN cc_start: 0.8497 (m-40) cc_final: 0.8288 (t0) REVERT: D 75 ARG cc_start: 0.7527 (ttm-80) cc_final: 0.7031 (ttm110) REVERT: D 96 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7288 (t0) REVERT: D 97 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7443 (t0) REVERT: D 179 MET cc_start: 0.8442 (tpt) cc_final: 0.7950 (tpt) REVERT: D 243 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6141 (mpt) REVERT: D 292 LYS cc_start: 0.8148 (mttt) cc_final: 0.7872 (mttp) REVERT: D 391 MET cc_start: 0.6703 (mtp) cc_final: 0.5647 (tpt) REVERT: B 222 LYS cc_start: 0.7970 (ptmm) cc_final: 0.7523 (pttt) REVERT: B 243 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.5868 (mpt) REVERT: B 292 LYS cc_start: 0.8110 (mttt) cc_final: 0.7784 (mttp) REVERT: C 75 ARG cc_start: 0.7456 (ttm-80) cc_final: 0.7142 (mtp-110) REVERT: C 96 ASP cc_start: 0.7990 (t0) cc_final: 0.7685 (t0) REVERT: C 97 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7392 (t0) REVERT: C 206 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7841 (mtmm) REVERT: C 243 MET cc_start: 0.7115 (OUTLIER) cc_final: 0.5890 (mpt) REVERT: C 401 ARG cc_start: 0.5938 (OUTLIER) cc_final: 0.5308 (tmt90) REVERT: C 420 PHE cc_start: 0.7256 (t80) cc_final: 0.7025 (t80) REVERT: E 34 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6900 (tpp) REVERT: E 75 ARG cc_start: 0.7604 (ttm-80) cc_final: 0.7166 (ttm110) REVERT: E 96 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7387 (t0) REVERT: E 97 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7569 (t0) REVERT: E 206 LYS cc_start: 0.8367 (mtpt) cc_final: 0.8100 (mmmm) REVERT: E 210 ASP cc_start: 0.7872 (m-30) cc_final: 0.7194 (t0) REVERT: E 262 MET cc_start: 0.4194 (mpp) cc_final: 0.3741 (mpp) REVERT: E 391 MET cc_start: 0.6801 (mtp) cc_final: 0.6572 (ttp) outliers start: 44 outliers final: 9 residues processed: 340 average time/residue: 1.0994 time to fit residues: 414.7363 Evaluate side-chains 294 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 272 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 168 CYS Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 168 CYS Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain B residue 168 CYS Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 168 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 124 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 141 ASN D 82 GLN D 85 ASN D 141 ASN D 219 ASN B 82 GLN B 85 ASN B 180 ASN C 82 GLN C 141 ASN C 219 ASN E 82 GLN E 141 ASN E 219 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14445 Z= 0.183 Angle : 0.688 12.675 19610 Z= 0.346 Chirality : 0.047 0.253 2260 Planarity : 0.004 0.049 2430 Dihedral : 8.332 59.281 2185 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.55 % Allowed : 15.91 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.82 (0.18), residues: 1710 helix: -2.17 (0.19), residues: 575 sheet: -0.54 (0.27), residues: 385 loop : -2.27 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 255 HIS 0.002 0.000 HIS C 125 PHE 0.011 0.001 PHE E 414 TYR 0.012 0.001 TYR A 144 ARG 0.009 0.001 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 293 time to evaluate : 1.608 Fit side-chains REVERT: A 69 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: A 75 ARG cc_start: 0.7520 (ttm-80) cc_final: 0.7089 (ttm110) REVERT: A 160 ASN cc_start: 0.7481 (OUTLIER) cc_final: 0.7264 (p0) REVERT: A 179 MET cc_start: 0.8531 (mmm) cc_final: 0.8182 (tpt) REVERT: A 206 LYS cc_start: 0.8287 (mtpt) cc_final: 0.8054 (mttt) REVERT: A 212 ARG cc_start: 0.7518 (ptp-110) cc_final: 0.7244 (ptp-110) REVERT: A 292 LYS cc_start: 0.8180 (mttt) cc_final: 0.7820 (mttp) REVERT: A 303 MET cc_start: 0.8824 (mmm) cc_final: 0.8576 (mmt) REVERT: D 62 ASN cc_start: 0.8490 (t0) cc_final: 0.8269 (t0) REVERT: D 75 ARG cc_start: 0.7651 (ttm-80) cc_final: 0.7134 (ttm110) REVERT: D 96 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7307 (t0) REVERT: D 97 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7446 (t0) REVERT: D 236 MET cc_start: 0.7647 (mmm) cc_final: 0.7445 (mmm) REVERT: D 292 LYS cc_start: 0.8197 (mttt) cc_final: 0.7935 (mttp) REVERT: D 303 MET cc_start: 0.9019 (mmt) cc_final: 0.8718 (mmt) REVERT: B 72 MET cc_start: 0.8836 (mtt) cc_final: 0.8632 (mtt) REVERT: B 96 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7409 (t0) REVERT: B 97 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7379 (t0) REVERT: B 179 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8347 (tpt) REVERT: B 210 ASP cc_start: 0.7760 (m-30) cc_final: 0.7459 (m-30) REVERT: B 292 LYS cc_start: 0.8138 (mttt) cc_final: 0.7816 (mttp) REVERT: C 75 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.7089 (ttm110) REVERT: C 243 MET cc_start: 0.7167 (OUTLIER) cc_final: 0.5943 (mpt) REVERT: C 391 MET cc_start: 0.5104 (tmm) cc_final: 0.4684 (tmm) REVERT: C 401 ARG cc_start: 0.5873 (OUTLIER) cc_final: 0.5313 (tmt90) REVERT: E 75 ARG cc_start: 0.7644 (ttm-80) cc_final: 0.7206 (ttm110) REVERT: E 96 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7551 (t0) REVERT: E 206 LYS cc_start: 0.8332 (mtpt) cc_final: 0.8103 (mmmm) REVERT: E 210 ASP cc_start: 0.7845 (m-30) cc_final: 0.7528 (m-30) REVERT: E 262 MET cc_start: 0.4506 (mpp) cc_final: 0.4131 (mpp) outliers start: 69 outliers final: 17 residues processed: 327 average time/residue: 0.9760 time to fit residues: 358.8203 Evaluate side-chains 298 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 271 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 120 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 0.3980 chunk 164 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN A 282 GLN D 219 ASN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 ASN E 219 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14445 Z= 0.191 Angle : 0.645 9.488 19610 Z= 0.326 Chirality : 0.046 0.172 2260 Planarity : 0.004 0.039 2430 Dihedral : 6.624 59.581 2185 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.41 % Allowed : 16.96 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.33 (0.19), residues: 1710 helix: -1.61 (0.20), residues: 575 sheet: -0.08 (0.29), residues: 345 loop : -2.14 (0.19), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 255 HIS 0.002 0.001 HIS C 125 PHE 0.012 0.001 PHE A 395 TYR 0.012 0.002 TYR E 317 ARG 0.007 0.001 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 289 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 ARG cc_start: 0.7574 (ttm-80) cc_final: 0.7163 (ttm110) REVERT: A 292 LYS cc_start: 0.8187 (mttt) cc_final: 0.7857 (mttp) REVERT: A 303 MET cc_start: 0.8845 (mmm) cc_final: 0.8585 (mmt) REVERT: A 401 ARG cc_start: 0.5545 (OUTLIER) cc_final: 0.5007 (tmt90) REVERT: A 420 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: D 75 ARG cc_start: 0.7686 (ttm-80) cc_final: 0.7163 (ttm110) REVERT: D 262 MET cc_start: 0.4232 (mpp) cc_final: 0.3932 (mpp) REVERT: D 292 LYS cc_start: 0.8235 (mttt) cc_final: 0.7996 (mttp) REVERT: D 303 MET cc_start: 0.9043 (mmt) cc_final: 0.8739 (mmt) REVERT: B 72 MET cc_start: 0.8830 (mtt) cc_final: 0.8561 (mtt) REVERT: B 96 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7631 (t0) REVERT: B 160 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7434 (OUTLIER) REVERT: B 164 ASP cc_start: 0.8653 (p0) cc_final: 0.8433 (p0) REVERT: B 179 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8428 (tpt) REVERT: B 210 ASP cc_start: 0.7764 (m-30) cc_final: 0.7472 (m-30) REVERT: B 227 GLU cc_start: 0.8159 (pt0) cc_final: 0.7886 (pt0) REVERT: B 243 MET cc_start: 0.6991 (OUTLIER) cc_final: 0.5909 (mpt) REVERT: B 292 LYS cc_start: 0.8189 (mttt) cc_final: 0.7869 (mttp) REVERT: C 28 GLU cc_start: 0.7463 (tp30) cc_final: 0.6895 (tp30) REVERT: C 49 LYS cc_start: 0.8720 (mttt) cc_final: 0.8188 (mmtt) REVERT: C 75 ARG cc_start: 0.7551 (ttm-80) cc_final: 0.7087 (ttm110) REVERT: C 96 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7600 (t0) REVERT: C 97 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7338 (t0) REVERT: C 227 GLU cc_start: 0.8363 (pt0) cc_final: 0.8106 (pt0) REVERT: C 243 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.5633 (mpt) REVERT: C 391 MET cc_start: 0.4838 (tmm) cc_final: 0.4300 (tmm) REVERT: C 401 ARG cc_start: 0.5892 (OUTLIER) cc_final: 0.5421 (tmt90) REVERT: E 75 ARG cc_start: 0.7636 (ttm-80) cc_final: 0.7219 (ttm110) REVERT: E 120 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7950 (ttmt) REVERT: E 156 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.6991 (mmt) REVERT: E 210 ASP cc_start: 0.7897 (m-30) cc_final: 0.7552 (m-30) REVERT: E 227 GLU cc_start: 0.8216 (pt0) cc_final: 0.7944 (pt0) REVERT: E 229 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7819 (mmm-85) REVERT: E 262 MET cc_start: 0.4465 (mpp) cc_final: 0.4156 (mpp) REVERT: E 391 MET cc_start: 0.6771 (ttp) cc_final: 0.6531 (tmm) outliers start: 82 outliers final: 16 residues processed: 327 average time/residue: 1.0162 time to fit residues: 371.5139 Evaluate side-chains 301 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 273 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 229 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 147 optimal weight: 0.5980 chunk 41 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN D 219 ASN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 219 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14445 Z= 0.203 Angle : 0.655 12.999 19610 Z= 0.330 Chirality : 0.045 0.161 2260 Planarity : 0.004 0.037 2430 Dihedral : 6.043 58.045 2185 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 5.54 % Allowed : 17.03 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -1.81 (0.19), residues: 1710 helix: -1.21 (0.21), residues: 575 sheet: 0.47 (0.30), residues: 320 loop : -1.87 (0.19), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 255 HIS 0.002 0.001 HIS C 125 PHE 0.015 0.001 PHE E 414 TYR 0.015 0.002 TYR A 144 ARG 0.005 0.000 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 286 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8750 (mttt) cc_final: 0.8252 (mtpt) REVERT: A 75 ARG cc_start: 0.7611 (ttm-80) cc_final: 0.7163 (ttm110) REVERT: A 225 CYS cc_start: 0.6112 (t) cc_final: 0.5883 (t) REVERT: A 292 LYS cc_start: 0.8227 (mttt) cc_final: 0.7895 (mttp) REVERT: A 303 MET cc_start: 0.8866 (mmm) cc_final: 0.8616 (mmt) REVERT: A 401 ARG cc_start: 0.5531 (OUTLIER) cc_final: 0.4950 (tmt90) REVERT: A 420 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7310 (m-80) REVERT: D 75 ARG cc_start: 0.7686 (ttm-80) cc_final: 0.7172 (ttm110) REVERT: D 97 ASP cc_start: 0.7706 (m-30) cc_final: 0.7421 (t0) REVERT: D 212 ARG cc_start: 0.7402 (ptp-110) cc_final: 0.7026 (ptp-110) REVERT: D 227 GLU cc_start: 0.8218 (pt0) cc_final: 0.7788 (pt0) REVERT: D 243 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.5935 (mpt) REVERT: D 262 MET cc_start: 0.4330 (mpp) cc_final: 0.4042 (mpp) REVERT: D 292 LYS cc_start: 0.8256 (mttt) cc_final: 0.8010 (mttp) REVERT: D 303 MET cc_start: 0.9053 (mmt) cc_final: 0.8765 (mmt) REVERT: D 420 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7128 (t80) REVERT: B 34 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6689 (tpp) REVERT: B 72 MET cc_start: 0.8832 (mtt) cc_final: 0.8622 (mtt) REVERT: B 210 ASP cc_start: 0.7764 (m-30) cc_final: 0.7478 (m-30) REVERT: B 227 GLU cc_start: 0.8160 (pt0) cc_final: 0.7894 (pt0) REVERT: B 243 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.5928 (mpt) REVERT: B 292 LYS cc_start: 0.8226 (mttt) cc_final: 0.7902 (mttp) REVERT: C 28 GLU cc_start: 0.7461 (tp30) cc_final: 0.6884 (tp30) REVERT: C 49 LYS cc_start: 0.8674 (mttt) cc_final: 0.8210 (mmtt) REVERT: C 75 ARG cc_start: 0.7552 (ttm-80) cc_final: 0.7071 (ttm110) REVERT: C 97 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7371 (t0) REVERT: C 229 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7421 (mmt90) REVERT: C 243 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.5593 (mpt) REVERT: C 391 MET cc_start: 0.4723 (tmm) cc_final: 0.4183 (tmm) REVERT: C 401 ARG cc_start: 0.5842 (OUTLIER) cc_final: 0.5510 (tmt90) REVERT: E 49 LYS cc_start: 0.8759 (mttt) cc_final: 0.8558 (mttt) REVERT: E 75 ARG cc_start: 0.7640 (ttm-80) cc_final: 0.7215 (ttm110) REVERT: E 96 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7637 (t0) REVERT: E 120 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7980 (ttmt) REVERT: E 130 ASP cc_start: 0.7892 (m-30) cc_final: 0.7618 (t0) REVERT: E 227 GLU cc_start: 0.8136 (pt0) cc_final: 0.7874 (pt0) REVERT: E 262 MET cc_start: 0.4541 (mpp) cc_final: 0.4109 (mpp) REVERT: E 268 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7189 (mtp180) outliers start: 84 outliers final: 29 residues processed: 327 average time/residue: 1.0747 time to fit residues: 392.1003 Evaluate side-chains 325 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 283 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 268 ARG Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 3.9990 chunk 147 optimal weight: 0.4980 chunk 32 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN D 219 ASN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 ASN E 282 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14445 Z= 0.186 Angle : 0.630 8.418 19610 Z= 0.318 Chirality : 0.044 0.154 2260 Planarity : 0.004 0.038 2430 Dihedral : 5.585 52.540 2185 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.81 % Allowed : 17.10 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -1.41 (0.20), residues: 1710 helix: -0.81 (0.21), residues: 580 sheet: 0.15 (0.28), residues: 365 loop : -1.51 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 255 HIS 0.002 0.001 HIS C 125 PHE 0.014 0.001 PHE E 414 TYR 0.013 0.001 TYR A 144 ARG 0.006 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 279 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8719 (mttt) cc_final: 0.8248 (mtpt) REVERT: A 75 ARG cc_start: 0.7590 (ttm-80) cc_final: 0.7145 (ttm110) REVERT: A 156 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7293 (mmt) REVERT: A 227 GLU cc_start: 0.8191 (pt0) cc_final: 0.7900 (tt0) REVERT: A 292 LYS cc_start: 0.8249 (mttt) cc_final: 0.7916 (mttp) REVERT: A 420 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.7283 (m-80) REVERT: D 75 ARG cc_start: 0.7722 (ttm-80) cc_final: 0.7200 (ttm110) REVERT: D 97 ASP cc_start: 0.7763 (m-30) cc_final: 0.7455 (t0) REVERT: D 212 ARG cc_start: 0.7380 (ptp-110) cc_final: 0.7045 (ptp-110) REVERT: D 243 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.5907 (mpt) REVERT: D 262 MET cc_start: 0.4375 (mpp) cc_final: 0.4136 (mpp) REVERT: D 292 LYS cc_start: 0.8282 (mttt) cc_final: 0.8041 (mttp) REVERT: D 303 MET cc_start: 0.9032 (mmt) cc_final: 0.8753 (mmt) REVERT: D 420 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.7153 (t80) REVERT: B 34 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6642 (tpp) REVERT: B 72 MET cc_start: 0.8833 (mtt) cc_final: 0.8567 (mtt) REVERT: B 97 ASP cc_start: 0.7844 (m-30) cc_final: 0.7468 (t0) REVERT: B 210 ASP cc_start: 0.7746 (m-30) cc_final: 0.7474 (m-30) REVERT: B 227 GLU cc_start: 0.8195 (pt0) cc_final: 0.7944 (pt0) REVERT: B 229 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8217 (mmm-85) REVERT: B 243 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.5889 (mpt) REVERT: B 292 LYS cc_start: 0.8232 (mttt) cc_final: 0.7908 (mttp) REVERT: C 49 LYS cc_start: 0.8689 (mttt) cc_final: 0.8210 (mmtt) REVERT: C 75 ARG cc_start: 0.7584 (ttm-80) cc_final: 0.7083 (ttm110) REVERT: C 97 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7435 (t0) REVERT: C 113 ASP cc_start: 0.8461 (p0) cc_final: 0.8220 (p0) REVERT: C 156 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.6452 (mmt) REVERT: C 163 MET cc_start: 0.8301 (mtm) cc_final: 0.7976 (mpp) REVERT: C 212 ARG cc_start: 0.7507 (ptp-110) cc_final: 0.7174 (ptp-170) REVERT: C 243 MET cc_start: 0.6898 (OUTLIER) cc_final: 0.5526 (mpt) REVERT: C 391 MET cc_start: 0.4692 (tmm) cc_final: 0.4194 (tmm) REVERT: C 401 ARG cc_start: 0.5906 (OUTLIER) cc_final: 0.5504 (tmt90) REVERT: E 75 ARG cc_start: 0.7647 (ttm-80) cc_final: 0.7215 (ttm110) REVERT: E 96 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7737 (t0) REVERT: E 120 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7993 (ttmt) REVERT: E 130 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7601 (t0) REVERT: E 156 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.6884 (mmt) REVERT: E 227 GLU cc_start: 0.8155 (pt0) cc_final: 0.7879 (pt0) REVERT: E 262 MET cc_start: 0.4558 (mpp) cc_final: 0.4120 (mpp) outliers start: 88 outliers final: 36 residues processed: 323 average time/residue: 1.0650 time to fit residues: 383.1919 Evaluate side-chains 320 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 269 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 0.0980 chunk 138 optimal weight: 0.0770 chunk 91 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 102 optimal weight: 0.0060 chunk 99 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** D 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 ASN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 219 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14445 Z= 0.146 Angle : 0.611 13.406 19610 Z= 0.307 Chirality : 0.043 0.159 2260 Planarity : 0.004 0.036 2430 Dihedral : 5.360 43.286 2185 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 4.62 % Allowed : 18.81 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 (0.20), residues: 1710 helix: -0.47 (0.21), residues: 580 sheet: 0.30 (0.29), residues: 360 loop : -1.37 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 255 HIS 0.002 0.001 HIS D 217 PHE 0.014 0.001 PHE E 414 TYR 0.015 0.001 TYR D 213 ARG 0.007 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 267 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.8734 (mttt) cc_final: 0.8305 (mmtt) REVERT: A 75 ARG cc_start: 0.7594 (ttm-80) cc_final: 0.7164 (ttm110) REVERT: A 179 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8139 (tpt) REVERT: A 243 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6283 (mtt) REVERT: A 260 ILE cc_start: 0.5078 (OUTLIER) cc_final: 0.4865 (pt) REVERT: A 292 LYS cc_start: 0.8220 (mttt) cc_final: 0.7892 (mttp) REVERT: D 75 ARG cc_start: 0.7730 (ttm-80) cc_final: 0.7221 (ttm110) REVERT: D 212 ARG cc_start: 0.7341 (ptp-110) cc_final: 0.6964 (ptp-170) REVERT: D 225 CYS cc_start: 0.6072 (t) cc_final: 0.5758 (t) REVERT: D 243 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.5932 (mpt) REVERT: D 292 LYS cc_start: 0.8240 (mttt) cc_final: 0.8001 (mttp) REVERT: D 420 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7176 (t80) REVERT: B 34 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6620 (tpp) REVERT: B 210 ASP cc_start: 0.7785 (m-30) cc_final: 0.7551 (m-30) REVERT: B 227 GLU cc_start: 0.8157 (pt0) cc_final: 0.7874 (pt0) REVERT: B 243 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.5831 (mpt) REVERT: B 292 LYS cc_start: 0.8188 (mttt) cc_final: 0.7875 (mttp) REVERT: C 49 LYS cc_start: 0.8679 (mttt) cc_final: 0.8238 (mmtt) REVERT: C 75 ARG cc_start: 0.7562 (ttm-80) cc_final: 0.7091 (ttm110) REVERT: C 163 MET cc_start: 0.8044 (mtm) cc_final: 0.7791 (mpp) REVERT: C 210 ASP cc_start: 0.7849 (m-30) cc_final: 0.7518 (m-30) REVERT: C 212 ARG cc_start: 0.7461 (ptp-110) cc_final: 0.7144 (ptp-170) REVERT: C 391 MET cc_start: 0.4725 (tmm) cc_final: 0.4304 (tmm) REVERT: C 401 ARG cc_start: 0.5843 (OUTLIER) cc_final: 0.5594 (tmt90) REVERT: E 49 LYS cc_start: 0.8720 (mttt) cc_final: 0.8218 (mmtt) REVERT: E 75 ARG cc_start: 0.7620 (ttm-80) cc_final: 0.7200 (ttm110) REVERT: E 120 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7971 (ttmt) REVERT: E 130 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7579 (t0) REVERT: E 227 GLU cc_start: 0.8060 (pt0) cc_final: 0.7823 (pt0) REVERT: E 262 MET cc_start: 0.4620 (mpp) cc_final: 0.4165 (mpp) outliers start: 70 outliers final: 35 residues processed: 300 average time/residue: 0.9778 time to fit residues: 329.6221 Evaluate side-chains 298 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 253 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN A 418 ASN D 219 ASN D 282 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 418 ASN C 77 ASN E 77 ASN E 219 ASN E 418 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14445 Z= 0.208 Angle : 0.634 9.460 19610 Z= 0.319 Chirality : 0.045 0.202 2260 Planarity : 0.004 0.035 2430 Dihedral : 5.328 47.140 2185 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.15 % Allowed : 19.08 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -0.98 (0.20), residues: 1710 helix: -0.23 (0.22), residues: 580 sheet: 0.12 (0.28), residues: 370 loop : -1.31 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 255 HIS 0.002 0.000 HIS C 125 PHE 0.012 0.001 PHE A 115 TYR 0.012 0.002 TYR B 144 ARG 0.006 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 289 time to evaluate : 4.327 Fit side-chains REVERT: A 28 GLU cc_start: 0.7553 (tp30) cc_final: 0.7113 (tp30) REVERT: A 49 LYS cc_start: 0.8726 (mttt) cc_final: 0.8371 (mmtt) REVERT: A 75 ARG cc_start: 0.7594 (ttm-80) cc_final: 0.7150 (ttm110) REVERT: A 179 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8096 (tpt) REVERT: A 227 GLU cc_start: 0.8087 (pt0) cc_final: 0.7816 (tt0) REVERT: A 292 LYS cc_start: 0.8271 (mttt) cc_final: 0.7940 (mttp) REVERT: D 75 ARG cc_start: 0.7729 (ttm-80) cc_final: 0.7206 (ttm110) REVERT: D 120 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7979 (ttmp) REVERT: D 212 ARG cc_start: 0.7436 (ptp-110) cc_final: 0.7073 (ptp-170) REVERT: D 225 CYS cc_start: 0.6261 (t) cc_final: 0.5968 (t) REVERT: D 420 PHE cc_start: 0.7535 (OUTLIER) cc_final: 0.7236 (t80) REVERT: B 28 GLU cc_start: 0.7700 (tp30) cc_final: 0.7044 (tp30) REVERT: B 34 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6591 (tpp) REVERT: B 210 ASP cc_start: 0.7775 (m-30) cc_final: 0.7528 (m-30) REVERT: B 227 GLU cc_start: 0.8233 (pt0) cc_final: 0.8027 (pt0) REVERT: B 229 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8261 (mmm-85) REVERT: B 292 LYS cc_start: 0.8210 (mttt) cc_final: 0.7927 (mttp) REVERT: C 28 GLU cc_start: 0.7494 (tp30) cc_final: 0.6918 (tp30) REVERT: C 49 LYS cc_start: 0.8684 (mttt) cc_final: 0.8209 (mmtt) REVERT: C 75 ARG cc_start: 0.7599 (ttm-80) cc_final: 0.7094 (ttm110) REVERT: C 97 ASP cc_start: 0.7670 (m-30) cc_final: 0.7416 (t0) REVERT: C 113 ASP cc_start: 0.8430 (p0) cc_final: 0.8195 (p0) REVERT: C 156 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.6327 (mmt) REVERT: C 163 MET cc_start: 0.8222 (mtm) cc_final: 0.7890 (mpp) REVERT: C 210 ASP cc_start: 0.7818 (m-30) cc_final: 0.7500 (m-30) REVERT: C 212 ARG cc_start: 0.7457 (ptp-110) cc_final: 0.7143 (ptp-170) REVERT: C 227 GLU cc_start: 0.8063 (pt0) cc_final: 0.7819 (tt0) REVERT: E 49 LYS cc_start: 0.8702 (mttt) cc_final: 0.8219 (mmtt) REVERT: E 75 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.7213 (ttm110) REVERT: E 96 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7808 (t0) REVERT: E 105 MET cc_start: 0.7215 (mtm) cc_final: 0.6994 (ptp) REVERT: E 120 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7984 (ttmt) REVERT: E 130 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7612 (t0) REVERT: E 156 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.6811 (mmt) REVERT: E 262 MET cc_start: 0.4590 (mpp) cc_final: 0.4172 (mpp) outliers start: 78 outliers final: 37 residues processed: 328 average time/residue: 1.1182 time to fit residues: 411.8167 Evaluate side-chains 329 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 282 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.6980 chunk 143 optimal weight: 0.0670 chunk 152 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 0.0570 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 0.0370 chunk 161 optimal weight: 3.9990 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 219 ASN D 77 ASN D 219 ASN D 282 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 418 ASN C 171 GLN E 219 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14445 Z= 0.164 Angle : 0.639 12.682 19610 Z= 0.321 Chirality : 0.044 0.182 2260 Planarity : 0.004 0.034 2430 Dihedral : 5.334 46.335 2185 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.70 % Allowed : 21.58 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -0.78 (0.20), residues: 1710 helix: 0.01 (0.22), residues: 580 sheet: 0.15 (0.28), residues: 365 loop : -1.21 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP E 255 HIS 0.002 0.001 HIS B 217 PHE 0.011 0.001 PHE E 414 TYR 0.011 0.001 TYR D 144 ARG 0.007 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 272 time to evaluate : 1.539 Fit side-chains REVERT: A 28 GLU cc_start: 0.7541 (tp30) cc_final: 0.7105 (tp30) REVERT: A 49 LYS cc_start: 0.8732 (mttt) cc_final: 0.8361 (mmtt) REVERT: A 75 ARG cc_start: 0.7589 (ttm-80) cc_final: 0.7152 (ttm110) REVERT: A 135 ARG cc_start: 0.7671 (ptp-170) cc_final: 0.7458 (mtm-85) REVERT: A 179 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8078 (tpt) REVERT: A 227 GLU cc_start: 0.7989 (pt0) cc_final: 0.7767 (tt0) REVERT: A 292 LYS cc_start: 0.8243 (mttt) cc_final: 0.7915 (mttp) REVERT: D 75 ARG cc_start: 0.7722 (ttm-80) cc_final: 0.7217 (ttm110) REVERT: D 120 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7986 (ttmp) REVERT: D 212 ARG cc_start: 0.7422 (ptp-110) cc_final: 0.7006 (ptp-170) REVERT: D 225 CYS cc_start: 0.6154 (t) cc_final: 0.5895 (t) REVERT: D 229 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7288 (mmt90) REVERT: D 420 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7191 (t80) REVERT: B 28 GLU cc_start: 0.7712 (tp30) cc_final: 0.7026 (tp30) REVERT: B 34 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6528 (tpp) REVERT: B 210 ASP cc_start: 0.7726 (m-30) cc_final: 0.7476 (m-30) REVERT: B 227 GLU cc_start: 0.8157 (pt0) cc_final: 0.7870 (pt0) REVERT: B 292 LYS cc_start: 0.8212 (mttt) cc_final: 0.7910 (mttp) REVERT: C 49 LYS cc_start: 0.8662 (mttt) cc_final: 0.8225 (mmtt) REVERT: C 75 ARG cc_start: 0.7568 (ttm-80) cc_final: 0.7095 (ttm110) REVERT: C 97 ASP cc_start: 0.7658 (m-30) cc_final: 0.7416 (t0) REVERT: C 113 ASP cc_start: 0.8425 (p0) cc_final: 0.8198 (p0) REVERT: C 163 MET cc_start: 0.8090 (mtm) cc_final: 0.7868 (mpp) REVERT: C 210 ASP cc_start: 0.7786 (m-30) cc_final: 0.7485 (m-30) REVERT: C 212 ARG cc_start: 0.7439 (ptp-110) cc_final: 0.7090 (ptp-170) REVERT: E 49 LYS cc_start: 0.8692 (mttt) cc_final: 0.8215 (mmtt) REVERT: E 75 ARG cc_start: 0.7632 (ttm-80) cc_final: 0.7216 (ttm110) REVERT: E 105 MET cc_start: 0.7249 (mtm) cc_final: 0.6958 (ptp) REVERT: E 120 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7959 (ttmt) REVERT: E 130 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7593 (t0) REVERT: E 156 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.6736 (mmt) REVERT: E 225 CYS cc_start: 0.6025 (t) cc_final: 0.5697 (t) REVERT: E 262 MET cc_start: 0.4688 (mpp) cc_final: 0.4235 (mpp) outliers start: 56 outliers final: 35 residues processed: 302 average time/residue: 1.0707 time to fit residues: 358.8613 Evaluate side-chains 309 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 266 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 120 LYS Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 169 optimal weight: 0.0980 chunk 155 optimal weight: 4.9990 chunk 134 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 104 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN D 77 ASN D 219 ASN D 282 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 418 ASN E 171 GLN E 219 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14445 Z= 0.192 Angle : 0.643 10.184 19610 Z= 0.323 Chirality : 0.044 0.160 2260 Planarity : 0.004 0.032 2430 Dihedral : 5.335 47.701 2185 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.63 % Allowed : 21.78 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -0.71 (0.20), residues: 1710 helix: 0.19 (0.22), residues: 580 sheet: 0.10 (0.28), residues: 370 loop : -1.22 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP E 255 HIS 0.002 0.000 HIS C 125 PHE 0.012 0.001 PHE A 115 TYR 0.015 0.001 TYR A 144 ARG 0.007 0.000 ARG A 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 274 time to evaluate : 1.633 Fit side-chains REVERT: A 49 LYS cc_start: 0.8724 (mttt) cc_final: 0.8287 (mmtt) REVERT: A 75 ARG cc_start: 0.7559 (ttm-80) cc_final: 0.7123 (ttm110) REVERT: A 135 ARG cc_start: 0.7704 (ptp-170) cc_final: 0.7460 (mtm-85) REVERT: A 227 GLU cc_start: 0.8027 (pt0) cc_final: 0.7796 (tt0) REVERT: A 292 LYS cc_start: 0.8275 (mttt) cc_final: 0.7944 (mttp) REVERT: D 75 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7209 (ttm110) REVERT: D 212 ARG cc_start: 0.7434 (ptp-110) cc_final: 0.7024 (ptp-170) REVERT: D 225 CYS cc_start: 0.6133 (t) cc_final: 0.5887 (t) REVERT: D 229 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7336 (mmt90) REVERT: D 420 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7234 (t80) REVERT: B 28 GLU cc_start: 0.7735 (tp30) cc_final: 0.7054 (tp30) REVERT: B 34 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6529 (tpp) REVERT: B 227 GLU cc_start: 0.8188 (pt0) cc_final: 0.7911 (pt0) REVERT: B 292 LYS cc_start: 0.8198 (mttt) cc_final: 0.7914 (mttp) REVERT: C 28 GLU cc_start: 0.7531 (tp30) cc_final: 0.6952 (tp30) REVERT: C 49 LYS cc_start: 0.8667 (mttt) cc_final: 0.8225 (mmtt) REVERT: C 75 ARG cc_start: 0.7585 (ttm-80) cc_final: 0.7092 (ttm110) REVERT: C 97 ASP cc_start: 0.7653 (m-30) cc_final: 0.7404 (t0) REVERT: C 113 ASP cc_start: 0.8423 (p0) cc_final: 0.8190 (p0) REVERT: C 156 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.6274 (mmt) REVERT: C 163 MET cc_start: 0.8146 (mtm) cc_final: 0.7910 (mpp) REVERT: C 210 ASP cc_start: 0.7766 (m-30) cc_final: 0.7470 (m-30) REVERT: C 212 ARG cc_start: 0.7428 (ptp-110) cc_final: 0.7123 (ptp-170) REVERT: C 227 GLU cc_start: 0.8109 (pt0) cc_final: 0.7880 (tt0) REVERT: C 243 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.5419 (mpt) REVERT: E 49 LYS cc_start: 0.8681 (mttt) cc_final: 0.8207 (mmtt) REVERT: E 75 ARG cc_start: 0.7641 (ttm-80) cc_final: 0.7223 (ttm110) REVERT: E 105 MET cc_start: 0.7314 (mtm) cc_final: 0.6980 (ptp) REVERT: E 120 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7960 (ttmt) REVERT: E 130 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7614 (t0) REVERT: E 156 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.6712 (mmt) REVERT: E 262 MET cc_start: 0.4730 (mpp) cc_final: 0.4272 (mpp) outliers start: 55 outliers final: 39 residues processed: 300 average time/residue: 1.0985 time to fit residues: 365.4416 Evaluate side-chains 320 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 273 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 269 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 19 optimal weight: 0.0040 chunk 37 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 138 optimal weight: 0.0670 chunk 17 optimal weight: 0.0770 chunk 24 optimal weight: 1.9990 chunk 118 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 overall best weight: 0.2888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN D 77 ASN D 180 ASN D 219 ASN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 ASN B 418 ASN C 58 ASN C 77 ASN C 282 GLN E 219 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.165922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.127091 restraints weight = 15189.738| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.17 r_work: 0.3271 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14445 Z= 0.153 Angle : 0.624 10.004 19610 Z= 0.311 Chirality : 0.043 0.162 2260 Planarity : 0.004 0.032 2430 Dihedral : 5.188 46.356 2185 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.43 % Allowed : 22.18 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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: -0.51 (0.20), residues: 1710 helix: 0.40 (0.22), residues: 580 sheet: 0.30 (0.28), residues: 360 loop : -1.19 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 255 HIS 0.002 0.000 HIS A 231 PHE 0.010 0.001 PHE A 115 TYR 0.011 0.001 TYR A 144 ARG 0.008 0.000 ARG A 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5924.04 seconds wall clock time: 110 minutes 7.12 seconds (6607.12 seconds total)