Starting phenix.real_space_refine on Sat Mar 16 08:17:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm2_20384/03_2024/6pm2_20384_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm2_20384/03_2024/6pm2_20384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm2_20384/03_2024/6pm2_20384.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm2_20384/03_2024/6pm2_20384.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm2_20384/03_2024/6pm2_20384_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pm2_20384/03_2024/6pm2_20384_updated.pdb" } resolution = 3.0 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= 0.062 sd= 2.734 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 105 5.16 5 C 9190 2.51 5 N 2265 2.21 5 O 2565 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 "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 "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 "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-5265/modules/chem_data/mon_lib" Total number of atoms: 14125 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2779 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2779 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2779 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2779 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2779 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 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: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'TAU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.29, per 1000 atoms: 0.52 Number of scatterers: 14125 At special positions: 0 Unit cell: (106.167, 104.521, 135.795, 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 105 16.00 O 2565 8.00 N 2265 7.00 C 9190 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=2.04 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=2.04 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=2.04 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=2.04 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=2.04 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 B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 5.41 Conformation dependent library (CDL) restraints added in 2.2 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... running ksdssp... Secondary structure from input PDB file: 56 helices and 25 sheets defined 35.8% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.555A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.584A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 239 through 242 No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 245 through 254 removed outlier: 3.978A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 287 removed outlier: 3.536A pdb=" N THR A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N MET A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 324 removed outlier: 4.092A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 427 removed outlier: 3.685A pdb=" N LEU A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.082A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 34 removed outlier: 3.536A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.569A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 239 through 242 No H-bonds generated for 'chain 'B' and resid 239 through 242' Processing helix chain 'B' and resid 245 through 254 removed outlier: 4.049A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'B' and resid 267 through 287 removed outlier: 3.537A pdb=" N THR B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 324 removed outlier: 4.084A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 399 removed outlier: 3.681A pdb=" N LEU B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 427 removed outlier: 3.506A pdb=" N VAL B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 4.087A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 34 removed outlier: 3.538A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.560A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 108 " --> pdb=" O MET C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 239 through 242 No H-bonds generated for 'chain 'C' and resid 239 through 242' Processing helix chain 'C' and resid 245 through 254 removed outlier: 4.063A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 258 No H-bonds generated for 'chain 'C' and resid 256 through 258' Processing helix chain 'C' and resid 267 through 287 removed outlier: 3.631A pdb=" N THR C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N MET C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 324 removed outlier: 4.055A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 399 removed outlier: 3.657A pdb=" N LEU C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 427 removed outlier: 4.603A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 4.067A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE C 427 " --> pdb=" O ILE C 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.516A pdb=" N ASP D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.598A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 239 through 242 No H-bonds generated for 'chain 'D' and resid 239 through 242' Processing helix chain 'D' and resid 245 through 254 removed outlier: 4.011A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 267 through 287 removed outlier: 3.591A pdb=" N THR D 274 " --> pdb=" O GLY D 270 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR D 278 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N MET D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 324 removed outlier: 4.108A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 427 removed outlier: 3.648A pdb=" N LEU D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 399 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE D 402 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 4.084A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 427 " --> pdb=" O ILE D 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 34 removed outlier: 3.579A pdb=" N ASP E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.574A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER E 108 " --> pdb=" O MET E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 239 through 242 No H-bonds generated for 'chain 'E' and resid 239 through 242' Processing helix chain 'E' and resid 245 through 254 removed outlier: 3.992A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 258 No H-bonds generated for 'chain 'E' and resid 256 through 258' Processing helix chain 'E' and resid 267 through 287 removed outlier: 3.669A pdb=" N THR E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR E 278 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N MET E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 324 removed outlier: 4.120A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 427 removed outlier: 3.633A pdb=" N LEU E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA E 399 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE E 402 " --> pdb=" O ARG E 398 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP E 403 " --> pdb=" O ALA E 399 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 4.043A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE E 427 " --> pdb=" O ILE E 423 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 182 through 186 removed outlier: 6.124A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 59 through 61 Processing sheet with id= C, first strand: chain 'A' and resid 98 through 100 Processing sheet with id= D, first strand: chain 'A' and resid 114 through 116 Processing sheet with id= E, first strand: chain 'A' and resid 211 through 213 Processing sheet with id= F, first strand: chain 'B' and resid 182 through 186 removed outlier: 6.121A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 59 through 61 Processing sheet with id= H, first strand: chain 'B' and resid 98 through 100 Processing sheet with id= I, first strand: chain 'B' and resid 114 through 116 Processing sheet with id= J, first strand: chain 'B' and resid 211 through 213 Processing sheet with id= K, first strand: chain 'C' and resid 182 through 186 removed outlier: 6.133A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 59 through 61 Processing sheet with id= M, first strand: chain 'C' and resid 98 through 100 Processing sheet with id= N, first strand: chain 'C' and resid 114 through 116 Processing sheet with id= O, first strand: chain 'C' and resid 211 through 213 Processing sheet with id= P, first strand: chain 'D' and resid 182 through 186 removed outlier: 6.168A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 59 through 61 Processing sheet with id= R, first strand: chain 'D' and resid 98 through 100 Processing sheet with id= S, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= T, first strand: chain 'D' and resid 211 through 213 Processing sheet with id= U, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.121A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 59 through 61 Processing sheet with id= W, first strand: chain 'E' and resid 98 through 100 Processing sheet with id= X, first strand: chain 'E' and resid 114 through 116 Processing sheet with id= Y, first strand: chain 'E' and resid 211 through 213 474 hydrogen bonds defined for protein. 1413 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: 4.52 Time building geometry restraints manager: 5.65 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: 4328 1.34 - 1.47: 3624 1.47 - 1.59: 6343 1.59 - 1.71: 0 1.71 - 1.83: 175 Bond restraints: 14470 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.51e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.40e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.36e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.17e+00 ... (remaining 14465 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.97: 544 106.97 - 113.74: 7958 113.74 - 120.50: 5585 120.50 - 127.26: 5393 127.26 - 134.03: 170 Bond angle restraints: 19650 Sorted by residual: angle pdb=" N VAL E 276 " pdb=" CA VAL E 276 " pdb=" C VAL E 276 " ideal model delta sigma weight residual 112.96 106.86 6.10 1.00e+00 1.00e+00 3.73e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 131.09 -9.55 1.91e+00 2.74e-01 2.50e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 131.09 -9.55 1.91e+00 2.74e-01 2.50e+01 angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 131.02 -9.48 1.91e+00 2.74e-01 2.47e+01 ... (remaining 19645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 8336 15.45 - 30.91: 368 30.91 - 46.36: 66 46.36 - 61.82: 43 61.82 - 77.27: 17 Dihedral angle restraints: 8830 sinusoidal: 3715 harmonic: 5115 Sorted by residual: dihedral pdb=" CA ASN C 160 " pdb=" C ASN C 160 " pdb=" N PHE C 161 " pdb=" CA PHE C 161 " ideal model delta harmonic sigma weight residual 180.00 -155.06 -24.94 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASN D 160 " pdb=" C ASN D 160 " pdb=" N PHE D 161 " pdb=" CA PHE D 161 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ASN B 160 " pdb=" C ASN B 160 " pdb=" N PHE B 161 " pdb=" CA PHE B 161 " ideal model delta harmonic sigma weight residual -180.00 -155.65 -24.35 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 8827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1579 0.050 - 0.100: 528 0.100 - 0.150: 124 0.150 - 0.200: 19 0.200 - 0.250: 10 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.56e+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 -2.52 0.25 2.00e-01 2.50e+01 1.56e+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 -2.52 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 2257 not shown) Planarity restraints: 2435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 410 " -0.047 5.00e-02 4.00e+02 7.12e-02 8.10e+00 pdb=" N PRO D 411 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 411 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 411 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 410 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO B 411 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 411 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 411 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 410 " 0.047 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO A 411 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " 0.039 5.00e-02 4.00e+02 ... (remaining 2432 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4492 2.84 - 3.36: 12235 3.36 - 3.87: 22669 3.87 - 4.39: 26594 4.39 - 4.90: 45274 Nonbonded interactions: 111264 Sorted by model distance: nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.330 2.440 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.335 2.440 nonbonded pdb=" OG SER D 145 " pdb=" O3 TAU D 504 " model vdw 2.336 2.440 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.336 2.440 nonbonded pdb=" OG SER C 145 " pdb=" O3 TAU C 504 " model vdw 2.337 2.440 ... (remaining 111259 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.340 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 38.870 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:10.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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 : 0.004 0.041 14470 Z= 0.288 Angle : 0.951 12.032 19650 Z= 0.475 Chirality : 0.054 0.250 2260 Planarity : 0.007 0.071 2430 Dihedral : 11.033 77.271 5480 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: -5.02 (0.15), residues: 1710 helix: -4.83 (0.07), residues: 530 sheet: -2.31 (0.22), residues: 385 loop : -2.63 (0.17), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 110 HIS 0.002 0.001 HIS A 125 PHE 0.019 0.002 PHE C 115 TYR 0.014 0.002 TYR A 74 ARG 0.004 0.001 ARG D 81 *********************** 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 455 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 455 time to evaluate : 1.733 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8986 (mtm-85) cc_final: 0.8748 (mtm180) REVERT: A 210 ASP cc_start: 0.7969 (m-30) cc_final: 0.7672 (m-30) REVERT: A 233 GLU cc_start: 0.7482 (tt0) cc_final: 0.7194 (mt-10) REVERT: A 398 ARG cc_start: 0.6876 (ttm110) cc_final: 0.6117 (tpp-160) REVERT: A 416 ILE cc_start: 0.8871 (tp) cc_final: 0.8621 (tp) REVERT: B 43 ARG cc_start: 0.8974 (mtm-85) cc_final: 0.8532 (mtm180) REVERT: B 75 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.7482 (ttp-110) REVERT: B 233 GLU cc_start: 0.7296 (tt0) cc_final: 0.7000 (mt-10) REVERT: B 398 ARG cc_start: 0.6762 (ttm110) cc_final: 0.5934 (tpp-160) REVERT: C 43 ARG cc_start: 0.9060 (mtm-85) cc_final: 0.8603 (mtm180) REVERT: C 75 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.7516 (ttm-80) REVERT: C 210 ASP cc_start: 0.8039 (m-30) cc_final: 0.7750 (m-30) REVERT: C 233 GLU cc_start: 0.7366 (tt0) cc_final: 0.7138 (mt-10) REVERT: C 398 ARG cc_start: 0.6726 (ttm110) cc_final: 0.5936 (tpp-160) REVERT: C 416 ILE cc_start: 0.8757 (tp) cc_final: 0.8541 (tp) REVERT: D 75 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7229 (ttm-80) REVERT: D 81 ARG cc_start: 0.7947 (mpt-90) cc_final: 0.6295 (mpp-170) REVERT: D 113 ASP cc_start: 0.8476 (p0) cc_final: 0.8216 (p0) REVERT: D 210 ASP cc_start: 0.8068 (m-30) cc_final: 0.7675 (m-30) REVERT: D 233 GLU cc_start: 0.7441 (tt0) cc_final: 0.7102 (mt-10) REVERT: D 398 ARG cc_start: 0.6913 (ttm110) cc_final: 0.6242 (tpp-160) REVERT: D 400 LYS cc_start: 0.6606 (tmtp) cc_final: 0.6338 (tmmt) REVERT: D 416 ILE cc_start: 0.8848 (tp) cc_final: 0.8498 (tp) REVERT: E 210 ASP cc_start: 0.8092 (m-30) cc_final: 0.7661 (m-30) REVERT: E 233 GLU cc_start: 0.7281 (tt0) cc_final: 0.7038 (mt-10) REVERT: E 398 ARG cc_start: 0.6714 (ttm110) cc_final: 0.6061 (tpp-160) REVERT: E 416 ILE cc_start: 0.8833 (tp) cc_final: 0.8624 (tp) outliers start: 0 outliers final: 2 residues processed: 455 average time/residue: 1.1217 time to fit residues: 562.7900 Evaluate side-chains 280 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 278 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain C residue 219 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 0.0270 chunk 154 optimal weight: 0.5980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 141 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 141 ASN B 180 ASN B 231 HIS ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 141 ASN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN D 141 ASN D 180 ASN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN ** D 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 141 ASN E 180 ASN ** E 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14470 Z= 0.186 Angle : 0.651 6.407 19650 Z= 0.332 Chirality : 0.045 0.149 2260 Planarity : 0.005 0.042 2430 Dihedral : 8.227 43.318 2194 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.08 % Allowed : 14.87 % Favored : 81.05 % 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: -3.79 (0.16), residues: 1710 helix: -3.14 (0.15), residues: 565 sheet: -1.21 (0.26), residues: 340 loop : -2.56 (0.18), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 84 HIS 0.002 0.001 HIS A 125 PHE 0.013 0.001 PHE C 414 TYR 0.026 0.001 TYR B 238 ARG 0.006 0.001 ARG D 229 *********************** 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 353 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 291 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8965 (mtm-85) cc_final: 0.8595 (mtm180) REVERT: A 71 THR cc_start: 0.9362 (p) cc_final: 0.9013 (p) REVERT: A 72 MET cc_start: 0.8975 (mtt) cc_final: 0.8532 (mtt) REVERT: A 227 GLU cc_start: 0.8492 (pt0) cc_final: 0.8089 (pt0) REVERT: A 233 GLU cc_start: 0.7097 (tt0) cc_final: 0.6823 (mt-10) REVERT: A 391 MET cc_start: 0.4165 (OUTLIER) cc_final: 0.3580 (tmm) REVERT: A 398 ARG cc_start: 0.6989 (ttm110) cc_final: 0.6427 (tpp-160) REVERT: B 28 GLU cc_start: 0.7925 (tp30) cc_final: 0.7547 (tm-30) REVERT: B 398 ARG cc_start: 0.6913 (ttm110) cc_final: 0.6334 (tpp-160) REVERT: C 28 GLU cc_start: 0.8004 (tp30) cc_final: 0.7645 (tm-30) REVERT: C 71 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.9080 (p) REVERT: C 210 ASP cc_start: 0.7894 (m-30) cc_final: 0.7567 (m-30) REVERT: D 28 GLU cc_start: 0.7955 (tt0) cc_final: 0.7555 (tm-30) REVERT: D 71 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9213 (p) REVERT: D 75 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7251 (ttm-80) REVERT: D 113 ASP cc_start: 0.8520 (p0) cc_final: 0.8269 (p0) REVERT: D 206 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8375 (mtpm) REVERT: D 210 ASP cc_start: 0.7953 (m-30) cc_final: 0.7555 (m-30) REVERT: D 398 ARG cc_start: 0.7105 (ttm110) cc_final: 0.6463 (tpp-160) REVERT: E 49 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8345 (mtmm) REVERT: E 210 ASP cc_start: 0.7922 (m-30) cc_final: 0.7525 (m-30) REVERT: E 398 ARG cc_start: 0.7099 (ttm110) cc_final: 0.6504 (tpp-160) outliers start: 62 outliers final: 16 residues processed: 327 average time/residue: 1.1225 time to fit residues: 404.6050 Evaluate side-chains 286 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 266 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 391 MET Chi-restraints excluded: chain E residue 404 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 128 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 153 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN B 131 ASN C 82 GLN D 62 ASN D 82 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN D 418 ASN E 85 ASN ** E 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14470 Z= 0.226 Angle : 0.637 10.941 19650 Z= 0.314 Chirality : 0.045 0.138 2260 Planarity : 0.004 0.040 2430 Dihedral : 6.514 30.321 2192 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 6.18 % Allowed : 14.80 % Favored : 79.01 % 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: -2.92 (0.18), residues: 1710 helix: -2.15 (0.19), residues: 545 sheet: -0.57 (0.27), residues: 340 loop : -2.38 (0.18), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 422 HIS 0.004 0.001 HIS A 125 PHE 0.014 0.001 PHE D 414 TYR 0.028 0.002 TYR A 238 ARG 0.006 0.001 ARG A 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 372 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 278 time to evaluate : 1.668 Fit side-chains REVERT: A 28 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7776 (tm-30) REVERT: A 43 ARG cc_start: 0.9061 (mtm-85) cc_final: 0.8596 (mtm180) REVERT: A 72 MET cc_start: 0.9014 (mtt) cc_final: 0.8744 (mtt) REVERT: A 233 GLU cc_start: 0.7239 (tt0) cc_final: 0.6907 (mt-10) REVERT: A 391 MET cc_start: 0.4420 (OUTLIER) cc_final: 0.3995 (tmm) REVERT: A 398 ARG cc_start: 0.7128 (ttm110) cc_final: 0.6526 (tpp-160) REVERT: B 233 GLU cc_start: 0.7194 (tt0) cc_final: 0.6852 (mt-10) REVERT: B 398 ARG cc_start: 0.6977 (ttm110) cc_final: 0.6422 (tpp-160) REVERT: C 28 GLU cc_start: 0.8003 (tp30) cc_final: 0.7616 (tm-30) REVERT: C 189 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8624 (mtpt) REVERT: C 206 LYS cc_start: 0.8641 (mtpt) cc_final: 0.8130 (mttp) REVERT: C 227 GLU cc_start: 0.8515 (pt0) cc_final: 0.8122 (pt0) REVERT: C 391 MET cc_start: 0.5394 (OUTLIER) cc_final: 0.4900 (tmm) REVERT: D 28 GLU cc_start: 0.7970 (tt0) cc_final: 0.7612 (tm-30) REVERT: D 75 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7409 (ttm-80) REVERT: D 206 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8237 (mttp) REVERT: D 235 GLN cc_start: 0.8378 (mm110) cc_final: 0.7993 (mt0) REVERT: D 395 PHE cc_start: 0.6599 (OUTLIER) cc_final: 0.6223 (m-80) REVERT: D 398 ARG cc_start: 0.7106 (ttm110) cc_final: 0.6504 (tpp-160) REVERT: D 400 LYS cc_start: 0.6573 (tmtp) cc_final: 0.6204 (tmmt) REVERT: E 233 GLU cc_start: 0.7191 (tt0) cc_final: 0.6794 (mt-10) REVERT: E 391 MET cc_start: 0.4586 (OUTLIER) cc_final: 0.4315 (tmm) REVERT: E 398 ARG cc_start: 0.7220 (ttm110) cc_final: 0.6562 (tpp-160) outliers start: 94 outliers final: 36 residues processed: 332 average time/residue: 1.1032 time to fit residues: 404.8299 Evaluate side-chains 289 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 248 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 391 MET Chi-restraints excluded: chain E residue 395 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.0870 chunk 116 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 62 ASN A 180 ASN A 231 HIS ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN D 85 ASN D 261 ASN E 261 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14470 Z= 0.351 Angle : 0.675 7.441 19650 Z= 0.338 Chirality : 0.046 0.153 2260 Planarity : 0.004 0.037 2430 Dihedral : 5.686 27.219 2192 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 6.51 % Allowed : 15.46 % Favored : 78.03 % 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: -2.45 (0.18), residues: 1710 helix: -1.53 (0.21), residues: 540 sheet: -0.34 (0.28), residues: 345 loop : -2.27 (0.18), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 422 HIS 0.004 0.001 HIS A 125 PHE 0.015 0.002 PHE A 124 TYR 0.026 0.002 TYR D 238 ARG 0.006 0.001 ARG A 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 359 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 260 time to evaluate : 1.842 Fit side-chains REVERT: A 28 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7665 (tm-30) REVERT: A 72 MET cc_start: 0.9071 (mtt) cc_final: 0.8825 (mtt) REVERT: A 233 GLU cc_start: 0.7308 (tt0) cc_final: 0.6947 (mt-10) REVERT: A 398 ARG cc_start: 0.7183 (ttm110) cc_final: 0.6516 (tpp-160) REVERT: B 97 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7490 (t0) REVERT: B 171 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8461 (mt0) REVERT: B 398 ARG cc_start: 0.6967 (ttm110) cc_final: 0.6277 (tpp-160) REVERT: C 28 GLU cc_start: 0.7952 (tp30) cc_final: 0.7610 (tm-30) REVERT: C 49 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8478 (mmtp) REVERT: C 126 GLU cc_start: 0.7426 (mm-30) cc_final: 0.7183 (mm-30) REVERT: C 189 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8605 (mtpt) REVERT: C 206 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8193 (mttm) REVERT: C 207 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: C 391 MET cc_start: 0.5291 (OUTLIER) cc_final: 0.4937 (tmm) REVERT: D 28 GLU cc_start: 0.7934 (tt0) cc_final: 0.7622 (tm-30) REVERT: D 75 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7339 (ttm-80) REVERT: D 113 ASP cc_start: 0.8653 (p0) cc_final: 0.8273 (p0) REVERT: D 207 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7709 (tm-30) REVERT: D 235 GLN cc_start: 0.8379 (mm110) cc_final: 0.7928 (mt0) REVERT: D 398 ARG cc_start: 0.7204 (ttm110) cc_final: 0.6600 (tpp-160) REVERT: D 400 LYS cc_start: 0.6507 (tmtp) cc_final: 0.6097 (tmmt) REVERT: E 206 LYS cc_start: 0.8827 (mtpt) cc_final: 0.8587 (mtpm) REVERT: E 233 GLU cc_start: 0.7308 (tt0) cc_final: 0.6919 (mt-10) REVERT: E 236 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7332 (tmm) REVERT: E 395 PHE cc_start: 0.6629 (OUTLIER) cc_final: 0.6134 (m-80) REVERT: E 398 ARG cc_start: 0.7239 (ttm110) cc_final: 0.6578 (tpp-160) outliers start: 99 outliers final: 50 residues processed: 311 average time/residue: 1.1620 time to fit residues: 399.3585 Evaluate side-chains 293 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 235 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 391 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 395 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 82 GLN A 180 ASN A 261 ASN B 58 ASN B 82 GLN B 261 ASN C 58 ASN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14470 Z= 0.297 Angle : 0.630 6.466 19650 Z= 0.319 Chirality : 0.045 0.137 2260 Planarity : 0.003 0.035 2430 Dihedral : 5.303 28.195 2192 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.59 % Allowed : 17.30 % Favored : 77.11 % 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: -2.10 (0.19), residues: 1710 helix: -1.17 (0.22), residues: 535 sheet: -0.20 (0.28), residues: 345 loop : -2.07 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 186 HIS 0.003 0.001 HIS A 125 PHE 0.014 0.002 PHE C 124 TYR 0.016 0.002 TYR D 238 ARG 0.007 0.001 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 333 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 248 time to evaluate : 1.502 Fit side-chains REVERT: A 36 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8572 (mtpm) REVERT: A 179 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8449 (tpt) REVERT: A 233 GLU cc_start: 0.7338 (tt0) cc_final: 0.7044 (mt-10) REVERT: A 395 PHE cc_start: 0.6885 (OUTLIER) cc_final: 0.6461 (m-10) REVERT: A 398 ARG cc_start: 0.7159 (ttm110) cc_final: 0.6605 (tpp-160) REVERT: B 97 ASP cc_start: 0.8082 (m-30) cc_final: 0.7533 (t0) REVERT: B 160 ASN cc_start: 0.7898 (OUTLIER) cc_final: 0.7468 (p0) REVERT: B 171 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8446 (mt0) REVERT: B 233 GLU cc_start: 0.7319 (tt0) cc_final: 0.6915 (mt-10) REVERT: B 398 ARG cc_start: 0.6968 (ttm110) cc_final: 0.6264 (tpp-160) REVERT: C 28 GLU cc_start: 0.7941 (tp30) cc_final: 0.7663 (tm-30) REVERT: C 49 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8472 (mmtp) REVERT: C 189 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8591 (mtpt) REVERT: C 206 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8181 (mttm) REVERT: C 207 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: C 227 GLU cc_start: 0.8526 (pt0) cc_final: 0.8195 (pt0) REVERT: C 391 MET cc_start: 0.5338 (OUTLIER) cc_final: 0.5040 (tmm) REVERT: D 28 GLU cc_start: 0.7926 (tt0) cc_final: 0.7698 (tm-30) REVERT: D 75 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7318 (ttm-80) REVERT: D 113 ASP cc_start: 0.8652 (p0) cc_final: 0.8292 (p0) REVERT: D 206 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8440 (mtpm) REVERT: D 207 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7750 (tm-30) REVERT: D 235 GLN cc_start: 0.8413 (mm110) cc_final: 0.7960 (mt0) REVERT: D 398 ARG cc_start: 0.7229 (ttm110) cc_final: 0.6619 (tpp-160) REVERT: E 189 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8559 (mtpt) REVERT: E 206 LYS cc_start: 0.8841 (mtpt) cc_final: 0.8591 (mtpm) REVERT: E 233 GLU cc_start: 0.7371 (tt0) cc_final: 0.6936 (mt-10) REVERT: E 301 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7871 (mt) REVERT: E 395 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.6371 (m-80) REVERT: E 398 ARG cc_start: 0.7249 (ttm110) cc_final: 0.6621 (tpp-160) outliers start: 85 outliers final: 45 residues processed: 303 average time/residue: 1.1504 time to fit residues: 384.7917 Evaluate side-chains 295 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 238 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 294 SER Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 395 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN C 62 ASN C 261 ASN D 62 ASN E 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14470 Z= 0.198 Angle : 0.596 9.421 19650 Z= 0.299 Chirality : 0.044 0.146 2260 Planarity : 0.003 0.036 2430 Dihedral : 4.927 27.030 2192 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.07 % Allowed : 18.82 % Favored : 76.12 % 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: -1.97 (0.19), residues: 1710 helix: -0.97 (0.23), residues: 545 sheet: -0.20 (0.28), residues: 345 loop : -2.02 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 186 HIS 0.002 0.000 HIS A 125 PHE 0.014 0.001 PHE A 258 TYR 0.014 0.001 TYR C 317 ARG 0.006 0.000 ARG D 229 *********************** 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 324 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 247 time to evaluate : 1.655 Fit side-chains REVERT: A 36 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8544 (mtpm) REVERT: A 97 ASP cc_start: 0.7823 (m-30) cc_final: 0.7093 (t0) REVERT: A 179 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8365 (tpt) REVERT: A 233 GLU cc_start: 0.7242 (tt0) cc_final: 0.6963 (mt-10) REVERT: A 395 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.6311 (m-10) REVERT: A 398 ARG cc_start: 0.7196 (ttm110) cc_final: 0.6658 (tpp-160) REVERT: B 97 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7510 (t0) REVERT: B 160 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7383 (p0) REVERT: B 398 ARG cc_start: 0.7044 (ttm110) cc_final: 0.6285 (tpp-160) REVERT: C 28 GLU cc_start: 0.8015 (tp30) cc_final: 0.7748 (tm-30) REVERT: C 49 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8470 (mmtp) REVERT: C 189 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8574 (mtpt) REVERT: C 206 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8154 (mttm) REVERT: C 207 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: C 235 GLN cc_start: 0.8333 (mt0) cc_final: 0.7938 (mt0) REVERT: C 308 LEU cc_start: 0.7917 (mp) cc_final: 0.7631 (tt) REVERT: C 391 MET cc_start: 0.5331 (OUTLIER) cc_final: 0.5023 (tmm) REVERT: D 75 ARG cc_start: 0.7872 (ttm-80) cc_final: 0.7313 (ttm-80) REVERT: D 156 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.7483 (mmt) REVERT: D 207 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: D 235 GLN cc_start: 0.8386 (mm110) cc_final: 0.7952 (mt0) REVERT: D 395 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.6541 (m-10) REVERT: D 398 ARG cc_start: 0.7221 (ttm110) cc_final: 0.6628 (tpp-160) REVERT: E 156 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.7425 (mmt) REVERT: E 189 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8522 (mtpt) REVERT: E 233 GLU cc_start: 0.7283 (tt0) cc_final: 0.6872 (mt-10) REVERT: E 395 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.6526 (m-80) REVERT: E 398 ARG cc_start: 0.7157 (ttm110) cc_final: 0.6604 (tpp-160) outliers start: 77 outliers final: 36 residues processed: 293 average time/residue: 1.0633 time to fit residues: 345.0150 Evaluate side-chains 289 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 238 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 395 PHE Chi-restraints excluded: chain E residue 408 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 138 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 0.3980 chunk 101 optimal weight: 0.9980 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 62 ASN B 62 ASN C 231 HIS D 62 ASN E 180 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14470 Z= 0.202 Angle : 0.609 13.419 19650 Z= 0.303 Chirality : 0.044 0.154 2260 Planarity : 0.003 0.035 2430 Dihedral : 4.746 25.592 2192 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.93 % Allowed : 19.34 % Favored : 75.72 % 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: -1.60 (0.19), residues: 1710 helix: -0.68 (0.23), residues: 560 sheet: 0.23 (0.29), residues: 320 loop : -1.86 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 84 HIS 0.002 0.000 HIS A 125 PHE 0.018 0.001 PHE A 258 TYR 0.013 0.001 TYR B 317 ARG 0.004 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 317 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 242 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8537 (mtpm) REVERT: A 97 ASP cc_start: 0.7779 (m-30) cc_final: 0.7080 (t0) REVERT: A 179 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8424 (tpt) REVERT: A 233 GLU cc_start: 0.7177 (tt0) cc_final: 0.6914 (mt-10) REVERT: A 391 MET cc_start: 0.4481 (OUTLIER) cc_final: 0.4197 (tmm) REVERT: A 395 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.6411 (m-10) REVERT: A 398 ARG cc_start: 0.7178 (ttm110) cc_final: 0.6647 (tpp-160) REVERT: B 97 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7541 (t0) REVERT: B 160 ASN cc_start: 0.7766 (OUTLIER) cc_final: 0.7344 (p0) REVERT: B 308 LEU cc_start: 0.7728 (mp) cc_final: 0.7383 (tt) REVERT: B 398 ARG cc_start: 0.6974 (ttm110) cc_final: 0.6221 (tpp-160) REVERT: C 28 GLU cc_start: 0.7956 (tp30) cc_final: 0.7697 (tm-30) REVERT: C 49 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8476 (mmtp) REVERT: C 189 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8548 (mtpt) REVERT: C 206 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8139 (mttm) REVERT: C 207 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: C 235 GLN cc_start: 0.8344 (mt0) cc_final: 0.7947 (mt0) REVERT: C 308 LEU cc_start: 0.7912 (mp) cc_final: 0.7645 (tt) REVERT: C 391 MET cc_start: 0.5268 (OUTLIER) cc_final: 0.4976 (tmm) REVERT: D 36 LYS cc_start: 0.8810 (mtpt) cc_final: 0.8587 (mtpp) REVERT: D 75 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7317 (ttm-80) REVERT: D 206 LYS cc_start: 0.8667 (mtpt) cc_final: 0.8398 (mtpm) REVERT: D 207 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7793 (tm-30) REVERT: D 235 GLN cc_start: 0.8380 (mm110) cc_final: 0.7924 (mt0) REVERT: D 308 LEU cc_start: 0.7800 (mp) cc_final: 0.7555 (tt) REVERT: D 395 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6600 (m-10) REVERT: D 398 ARG cc_start: 0.7210 (ttm110) cc_final: 0.6641 (tpp-160) REVERT: E 24 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.5786 (mpp) REVERT: E 28 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7338 (pp20) REVERT: E 156 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.7348 (mmt) REVERT: E 189 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8513 (mtpt) REVERT: E 233 GLU cc_start: 0.7279 (tt0) cc_final: 0.6875 (mt-10) REVERT: E 398 ARG cc_start: 0.7074 (ttm110) cc_final: 0.6582 (tpp-160) outliers start: 75 outliers final: 40 residues processed: 286 average time/residue: 1.0888 time to fit residues: 345.0974 Evaluate side-chains 297 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 242 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 395 PHE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 283 SER Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 395 PHE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 180 ASN Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 408 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 104 optimal weight: 0.0670 chunk 111 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN D 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14470 Z= 0.261 Angle : 0.627 11.783 19650 Z= 0.313 Chirality : 0.045 0.168 2260 Planarity : 0.003 0.035 2430 Dihedral : 4.765 25.925 2192 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.80 % Allowed : 19.80 % Favored : 75.39 % 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: -1.51 (0.20), residues: 1710 helix: -0.60 (0.23), residues: 560 sheet: 0.32 (0.29), residues: 320 loop : -1.84 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 84 HIS 0.002 0.000 HIS A 125 PHE 0.015 0.001 PHE C 258 TYR 0.013 0.001 TYR B 317 ARG 0.005 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 310 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 237 time to evaluate : 1.764 Fit side-chains revert: symmetry clash REVERT: A 36 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8565 (mtpm) REVERT: A 97 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7085 (t0) REVERT: A 233 GLU cc_start: 0.7221 (tt0) cc_final: 0.6927 (mt-10) REVERT: A 308 LEU cc_start: 0.7710 (mp) cc_final: 0.7384 (tt) REVERT: A 398 ARG cc_start: 0.7148 (ttm110) cc_final: 0.6525 (tpp-160) REVERT: B 96 ASP cc_start: 0.8517 (m-30) cc_final: 0.8257 (m-30) REVERT: B 97 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7556 (t0) REVERT: B 160 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7373 (p0) REVERT: B 233 GLU cc_start: 0.7381 (tt0) cc_final: 0.6986 (mt-10) REVERT: B 308 LEU cc_start: 0.7722 (mp) cc_final: 0.7395 (tt) REVERT: B 398 ARG cc_start: 0.7010 (ttm110) cc_final: 0.6201 (tpp-160) REVERT: C 28 GLU cc_start: 0.7952 (tp30) cc_final: 0.7690 (tm-30) REVERT: C 189 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8562 (mtpt) REVERT: C 206 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8125 (mttm) REVERT: C 207 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7832 (tm-30) REVERT: C 235 GLN cc_start: 0.8356 (mt0) cc_final: 0.7932 (mt0) REVERT: C 308 LEU cc_start: 0.7885 (mp) cc_final: 0.7650 (tt) REVERT: C 391 MET cc_start: 0.5190 (OUTLIER) cc_final: 0.4920 (tmm) REVERT: D 75 ARG cc_start: 0.7846 (ttm-80) cc_final: 0.7271 (ttm-80) REVERT: D 156 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.7525 (mmt) REVERT: D 206 LYS cc_start: 0.8663 (mtpt) cc_final: 0.8440 (mtpm) REVERT: D 207 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7808 (tm-30) REVERT: D 235 GLN cc_start: 0.8403 (mm110) cc_final: 0.7984 (mt0) REVERT: D 308 LEU cc_start: 0.7792 (mp) cc_final: 0.7575 (tt) REVERT: D 398 ARG cc_start: 0.7223 (ttm110) cc_final: 0.6629 (tpp-160) REVERT: E 24 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7156 (tpt) REVERT: E 28 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7298 (tm-30) REVERT: E 156 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.7550 (mmt) REVERT: E 189 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8477 (mtpt) REVERT: E 233 GLU cc_start: 0.7357 (tt0) cc_final: 0.6954 (mt-10) REVERT: E 398 ARG cc_start: 0.7209 (ttm110) cc_final: 0.6596 (tpp-160) outliers start: 73 outliers final: 46 residues processed: 281 average time/residue: 1.1089 time to fit residues: 344.5662 Evaluate side-chains 285 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 228 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 107 ASP 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 170 MET Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 97 ASP 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 219 ASN Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 189 LYS Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 189 LYS Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 294 SER Chi-restraints excluded: chain E residue 408 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 152 optimal weight: 0.0040 chunk 91 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 144 optimal weight: 0.0770 chunk 100 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN D 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14470 Z= 0.179 Angle : 0.596 12.279 19650 Z= 0.298 Chirality : 0.043 0.145 2260 Planarity : 0.003 0.033 2430 Dihedral : 4.521 23.783 2192 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.95 % Allowed : 21.18 % Favored : 74.87 % 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: -1.36 (0.20), residues: 1710 helix: -0.43 (0.22), residues: 580 sheet: 0.36 (0.29), residues: 320 loop : -1.79 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 186 HIS 0.001 0.000 HIS A 125 PHE 0.014 0.001 PHE C 258 TYR 0.012 0.001 TYR B 317 ARG 0.005 0.000 ARG D 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 292 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 232 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7608 (OUTLIER) cc_final: 0.7039 (t0) REVERT: A 233 GLU cc_start: 0.7140 (tt0) cc_final: 0.6897 (mt-10) REVERT: A 398 ARG cc_start: 0.7034 (ttm110) cc_final: 0.6428 (tpp-160) REVERT: B 97 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7593 (t0) REVERT: B 160 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7340 (p0) REVERT: B 233 GLU cc_start: 0.7309 (tt0) cc_final: 0.6937 (mt-10) REVERT: B 308 LEU cc_start: 0.7691 (mp) cc_final: 0.7426 (tt) REVERT: B 398 ARG cc_start: 0.6922 (ttm110) cc_final: 0.6106 (tpp-160) REVERT: C 28 GLU cc_start: 0.7901 (tp30) cc_final: 0.7616 (tm-30) REVERT: C 206 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8088 (mttm) REVERT: C 207 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: C 235 GLN cc_start: 0.8357 (mt0) cc_final: 0.7959 (mt0) REVERT: C 391 MET cc_start: 0.5289 (OUTLIER) cc_final: 0.5011 (tmm) REVERT: D 75 ARG cc_start: 0.7859 (ttm-80) cc_final: 0.7281 (ttm-80) REVERT: D 156 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.7383 (mmt) REVERT: D 207 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: E 24 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.5789 (mpp) REVERT: E 28 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7456 (pp20) REVERT: E 97 ASP cc_start: 0.7888 (m-30) cc_final: 0.7267 (t0) REVERT: E 171 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8516 (mt0) REVERT: E 398 ARG cc_start: 0.7202 (ttm110) cc_final: 0.6550 (tpp-160) outliers start: 60 outliers final: 33 residues processed: 268 average time/residue: 1.0644 time to fit residues: 316.8014 Evaluate side-chains 276 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 234 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 107 ASP 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 294 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 97 ASP 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 219 ASN Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 283 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 155 optimal weight: 0.3980 chunk 134 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 104 optimal weight: 0.1980 chunk 82 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 180 ASN B 180 ASN D 62 ASN D 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14470 Z= 0.183 Angle : 0.605 12.073 19650 Z= 0.302 Chirality : 0.044 0.148 2260 Planarity : 0.003 0.034 2430 Dihedral : 4.554 37.745 2192 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.16 % Allowed : 22.24 % Favored : 74.61 % 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: -1.20 (0.20), residues: 1710 helix: -0.23 (0.23), residues: 580 sheet: 0.48 (0.29), residues: 320 loop : -1.76 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 84 HIS 0.001 0.000 HIS A 125 PHE 0.015 0.001 PHE C 258 TYR 0.012 0.001 TYR B 317 ARG 0.004 0.000 ARG D 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 274 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 226 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.7511 (m-30) cc_final: 0.7013 (t0) REVERT: A 398 ARG cc_start: 0.7019 (ttm110) cc_final: 0.6397 (tpp-160) REVERT: B 97 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7599 (t0) REVERT: B 160 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7359 (p0) REVERT: B 233 GLU cc_start: 0.7309 (tt0) cc_final: 0.6951 (mt-10) REVERT: B 308 LEU cc_start: 0.7699 (mp) cc_final: 0.7463 (tt) REVERT: B 398 ARG cc_start: 0.6918 (ttm110) cc_final: 0.6045 (tpp-160) REVERT: C 28 GLU cc_start: 0.7905 (tp30) cc_final: 0.7559 (tm-30) REVERT: C 206 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8090 (mttm) REVERT: C 207 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: C 235 GLN cc_start: 0.8368 (mt0) cc_final: 0.7967 (mt0) REVERT: C 391 MET cc_start: 0.5274 (OUTLIER) cc_final: 0.4979 (tmm) REVERT: D 75 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7286 (ttm-80) REVERT: D 156 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.7465 (mmt) REVERT: D 207 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7808 (tm-30) REVERT: E 24 MET cc_start: 0.7471 (tpt) cc_final: 0.5789 (mpp) REVERT: E 28 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7462 (pp20) REVERT: E 97 ASP cc_start: 0.7870 (m-30) cc_final: 0.7288 (t0) REVERT: E 171 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8555 (mt0) REVERT: E 233 GLU cc_start: 0.7257 (tt0) cc_final: 0.6897 (mt-10) REVERT: E 398 ARG cc_start: 0.7177 (ttm110) cc_final: 0.6529 (tpp-160) outliers start: 48 outliers final: 34 residues processed: 259 average time/residue: 1.0813 time to fit residues: 310.3133 Evaluate side-chains 260 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 220 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 107 ASP 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 294 SER Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 170 MET Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 401 ARG Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 227 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 118 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 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 62 ASN A 180 ASN B 180 ASN D 62 ASN D 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.110985 restraints weight = 16982.128| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.28 r_work: 0.3106 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14470 Z= 0.194 Angle : 0.605 12.225 19650 Z= 0.301 Chirality : 0.044 0.156 2260 Planarity : 0.003 0.035 2430 Dihedral : 4.558 44.486 2190 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.55 % Allowed : 22.30 % Favored : 74.14 % 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: -1.10 (0.20), residues: 1710 helix: -0.10 (0.23), residues: 580 sheet: 0.51 (0.29), residues: 320 loop : -1.74 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 255 HIS 0.002 0.000 HIS A 125 PHE 0.015 0.001 PHE C 258 TYR 0.012 0.001 TYR B 317 ARG 0.005 0.000 ARG D 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5906.43 seconds wall clock time: 107 minutes 4.89 seconds (6424.89 seconds total)