Starting phenix.real_space_refine on Sat Mar 16 09:25:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plx_20379/03_2024/6plx_20379_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plx_20379/03_2024/6plx_20379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plx_20379/03_2024/6plx_20379.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plx_20379/03_2024/6plx_20379.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plx_20379/03_2024/6plx_20379_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plx_20379/03_2024/6plx_20379_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.061 sd= 2.930 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9270 2.51 5 N 2290 2.21 5 O 2580 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 PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 325": "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: 14240 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2802 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 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: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.02, per 1000 atoms: 0.56 Number of scatterers: 14240 At special positions: 0 Unit cell: (107.813, 105.344, 136.618, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2580 8.00 N 2290 7.00 C 9270 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: 5.23 Conformation dependent library (CDL) restraints added in 2.6 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: 55 helices and 25 sheets defined 33.5% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.530A 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 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' 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 246 through 255 removed outlier: 3.810A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 287 removed outlier: 3.540A pdb=" N VAL A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG A 287 " --> pdb=" O SER A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 326 removed outlier: 4.304A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 401 removed outlier: 3.931A pdb=" N LEU A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 424 removed outlier: 3.783A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.292A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 34 removed outlier: 3.530A 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 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' 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 246 through 255 removed outlier: 3.810A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 287 removed outlier: 3.540A pdb=" N VAL B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR B 280 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG B 287 " --> pdb=" O SER B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 326 removed outlier: 4.305A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 401 removed outlier: 3.931A pdb=" N LEU B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 424 removed outlier: 3.784A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 4.291A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 34 removed outlier: 3.531A 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 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' 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 246 through 255 removed outlier: 3.809A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 287 removed outlier: 3.540A pdb=" N VAL C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG C 287 " --> pdb=" O SER C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 326 removed outlier: 4.305A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR C 317 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 401 removed outlier: 3.931A pdb=" N LEU C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 424 removed outlier: 3.783A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 4.291A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE C 416 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.531A 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 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' 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 246 through 255 removed outlier: 3.809A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 287 removed outlier: 3.539A pdb=" N VAL D 269 " --> pdb=" O ALA D 265 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG D 287 " --> pdb=" O SER D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 326 removed outlier: 4.303A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR D 317 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 401 removed outlier: 3.931A pdb=" N LEU D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 424 removed outlier: 3.783A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 4.290A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 34 removed outlier: 3.531A 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 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' 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 246 through 255 removed outlier: 3.809A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 287 removed outlier: 3.540A pdb=" N VAL E 269 " --> pdb=" O ALA E 265 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR E 280 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG E 287 " --> pdb=" O SER E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 326 removed outlier: 4.305A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR E 317 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 401 removed outlier: 3.931A pdb=" N LEU E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 424 removed outlier: 3.784A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 4.291A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 182 through 186 removed outlier: 6.157A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.798A 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 210 through 213 Processing sheet with id= F, first strand: chain 'B' and resid 182 through 186 removed outlier: 6.158A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.798A 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 210 through 213 Processing sheet with id= K, first strand: chain 'C' and resid 182 through 186 removed outlier: 6.158A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.798A 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 210 through 213 Processing sheet with id= P, first strand: chain 'D' and resid 182 through 186 removed outlier: 6.157A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.799A 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 210 through 213 Processing sheet with id= U, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.158A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.797A 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 210 through 213 480 hydrogen bonds defined for protein. 1425 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: 4.02 Time building geometry restraints manager: 5.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4296 1.34 - 1.46: 3614 1.46 - 1.58: 6505 1.58 - 1.70: 0 1.70 - 1.83: 170 Bond restraints: 14585 Sorted by residual: bond pdb=" CB ARG C 234 " pdb=" CG ARG C 234 " ideal model delta sigma weight residual 1.520 1.458 0.062 3.00e-02 1.11e+03 4.22e+00 bond pdb=" CB ARG A 234 " pdb=" CG ARG A 234 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.20e+00 bond pdb=" CB ARG B 234 " pdb=" CG ARG B 234 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.19e+00 bond pdb=" CB ARG D 234 " pdb=" CG ARG D 234 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.18e+00 bond pdb=" CB ARG E 234 " pdb=" CG ARG E 234 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.11e+00 ... (remaining 14580 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.73: 383 105.73 - 112.92: 7682 112.92 - 120.11: 5674 120.11 - 127.30: 5871 127.30 - 134.50: 165 Bond angle restraints: 19775 Sorted by residual: angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 134.50 -12.96 1.91e+00 2.74e-01 4.60e+01 angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 134.46 -12.92 1.91e+00 2.74e-01 4.57e+01 angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 134.44 -12.90 1.91e+00 2.74e-01 4.56e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 134.44 -12.90 1.91e+00 2.74e-01 4.56e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 134.42 -12.88 1.91e+00 2.74e-01 4.54e+01 ... (remaining 19770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.20: 8637 21.20 - 42.40: 218 42.40 - 63.61: 20 63.61 - 84.81: 35 84.81 - 106.01: 20 Dihedral angle restraints: 8930 sinusoidal: 3815 harmonic: 5115 Sorted by residual: 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 -152.19 -27.81 0 5.00e+00 4.00e-02 3.09e+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 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ASN A 160 " pdb=" C ASN A 160 " pdb=" N PHE A 161 " pdb=" CA PHE A 161 " ideal model delta harmonic sigma weight residual -180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 8927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1580 0.059 - 0.118: 556 0.118 - 0.178: 99 0.178 - 0.237: 15 0.237 - 0.296: 15 Chirality restraints: 2265 Sorted by residual: 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 -2.57 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 2262 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 102 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO B 103 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 103 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 103 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 102 " 0.042 5.00e-02 4.00e+02 6.30e-02 6.36e+00 pdb=" N PRO E 103 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 102 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO D 103 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.035 5.00e-02 4.00e+02 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 4519 2.83 - 3.35: 12107 3.35 - 3.87: 22723 3.87 - 4.38: 27254 4.38 - 4.90: 46058 Nonbonded interactions: 112661 Sorted by model distance: nonbonded pdb=" OE2 GLU D 69 " pdb=" NH2 ARG D 234 " model vdw 2.316 2.520 nonbonded pdb=" OE2 GLU B 69 " pdb=" NH2 ARG B 234 " model vdw 2.316 2.520 nonbonded pdb=" OE2 GLU A 69 " pdb=" NH2 ARG A 234 " model vdw 2.317 2.520 nonbonded pdb=" OE2 GLU C 69 " pdb=" NH2 ARG C 234 " model vdw 2.317 2.520 nonbonded pdb=" OE2 GLU E 69 " pdb=" NH2 ARG E 234 " model vdw 2.317 2.520 ... (remaining 112656 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.290 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 39.800 Find NCS groups from input model: 0.930 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:10.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.011 0.076 14585 Z= 0.679 Angle : 1.134 12.956 19775 Z= 0.577 Chirality : 0.065 0.296 2265 Planarity : 0.008 0.063 2450 Dihedral : 13.133 106.011 5580 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % 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: -5.10 (0.15), residues: 1710 helix: -4.69 (0.08), residues: 585 sheet: -2.54 (0.22), residues: 395 loop : -2.48 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 302 HIS 0.003 0.002 HIS D 231 PHE 0.023 0.003 PHE B 258 TYR 0.017 0.003 TYR E 144 ARG 0.008 0.002 ARG A 135 *********************** 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 469 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 469 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8376 (ptt) cc_final: 0.7773 (ptm) REVERT: A 102 ASP cc_start: 0.8147 (t0) cc_final: 0.7921 (t0) REVERT: A 104 SER cc_start: 0.9212 (t) cc_final: 0.8978 (p) REVERT: A 126 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7570 (pm20) REVERT: A 130 ASP cc_start: 0.8072 (m-30) cc_final: 0.7712 (m-30) REVERT: A 227 GLU cc_start: 0.8578 (pt0) cc_final: 0.8315 (pt0) REVERT: A 233 GLU cc_start: 0.7814 (tt0) cc_final: 0.7211 (mt-10) REVERT: A 316 GLU cc_start: 0.7248 (tm-30) cc_final: 0.6569 (tm-30) REVERT: A 391 MET cc_start: 0.7013 (mmm) cc_final: 0.6790 (mmm) REVERT: A 398 ARG cc_start: 0.7801 (ttm170) cc_final: 0.7081 (tpp-160) REVERT: B 24 MET cc_start: 0.8215 (ptt) cc_final: 0.7351 (ptm) REVERT: B 157 ASP cc_start: 0.8535 (t0) cc_final: 0.8320 (t70) REVERT: B 181 ASP cc_start: 0.8211 (m-30) cc_final: 0.7906 (m-30) REVERT: B 311 PHE cc_start: 0.7333 (t80) cc_final: 0.7126 (t80) REVERT: B 316 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6557 (tm-30) REVERT: B 391 MET cc_start: 0.6833 (mmm) cc_final: 0.6606 (mmm) REVERT: B 398 ARG cc_start: 0.7892 (ttm170) cc_final: 0.7319 (tpp-160) REVERT: C 24 MET cc_start: 0.8287 (ptt) cc_final: 0.7417 (ptm) REVERT: C 96 ASP cc_start: 0.8465 (m-30) cc_final: 0.8153 (m-30) REVERT: C 138 LYS cc_start: 0.8822 (mtpt) cc_final: 0.8429 (mttt) REVERT: C 233 GLU cc_start: 0.7786 (tt0) cc_final: 0.7571 (tt0) REVERT: C 311 PHE cc_start: 0.7324 (t80) cc_final: 0.7082 (t80) REVERT: C 316 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6980 (tm-30) REVERT: C 398 ARG cc_start: 0.7868 (ttm170) cc_final: 0.7237 (tpp-160) REVERT: D 24 MET cc_start: 0.8410 (ptt) cc_final: 0.7613 (ptt) REVERT: D 157 ASP cc_start: 0.8537 (t0) cc_final: 0.8286 (t70) REVERT: D 311 PHE cc_start: 0.7408 (t80) cc_final: 0.7053 (t80) REVERT: D 316 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6740 (tm-30) REVERT: D 398 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7259 (tpp-160) REVERT: E 24 MET cc_start: 0.8424 (ptt) cc_final: 0.7916 (ptt) REVERT: E 72 MET cc_start: 0.8890 (mtm) cc_final: 0.8588 (mtm) REVERT: E 181 ASP cc_start: 0.8267 (m-30) cc_final: 0.8009 (m-30) REVERT: E 208 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7887 (pp20) REVERT: E 233 GLU cc_start: 0.7751 (tt0) cc_final: 0.7118 (mt-10) REVERT: E 311 PHE cc_start: 0.7275 (t80) cc_final: 0.7033 (t80) REVERT: E 316 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6862 (tm-30) REVERT: E 398 ARG cc_start: 0.7794 (ttm170) cc_final: 0.7101 (tpp-160) outliers start: 0 outliers final: 1 residues processed: 469 average time/residue: 1.0540 time to fit residues: 548.2068 Evaluate side-chains 288 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 287 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E 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: 1.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 chunk 154 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 141 ASN A 231 HIS B 62 ASN B 82 GLN B 141 ASN B 180 ASN B 231 HIS C 62 ASN C 82 GLN C 141 ASN C 231 HIS D 62 ASN D 82 GLN D 141 ASN D 180 ASN D 231 HIS E 62 ASN E 82 GLN E 141 ASN E 180 ASN E 231 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14585 Z= 0.217 Angle : 0.694 8.468 19775 Z= 0.347 Chirality : 0.047 0.175 2265 Planarity : 0.005 0.044 2450 Dihedral : 10.004 61.334 2202 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.29 % Allowed : 15.16 % Favored : 81.55 % 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: -3.74 (0.17), residues: 1710 helix: -3.21 (0.15), residues: 590 sheet: -1.69 (0.27), residues: 345 loop : -2.10 (0.18), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 422 HIS 0.003 0.001 HIS C 231 PHE 0.014 0.001 PHE E 414 TYR 0.009 0.001 TYR E 218 ARG 0.007 0.001 ARG B 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 352 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 301 time to evaluate : 1.878 Fit side-chains REVERT: A 227 GLU cc_start: 0.8479 (pt0) cc_final: 0.8275 (pt0) REVERT: A 233 GLU cc_start: 0.7441 (tt0) cc_final: 0.6983 (mt-10) REVERT: A 243 MET cc_start: 0.8337 (mtm) cc_final: 0.8106 (ptp) REVERT: A 316 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6424 (tm-30) REVERT: A 391 MET cc_start: 0.6948 (mmm) cc_final: 0.6721 (mmm) REVERT: A 398 ARG cc_start: 0.7664 (ttm170) cc_final: 0.7025 (tpp-160) REVERT: B 24 MET cc_start: 0.7799 (ptt) cc_final: 0.7574 (ptt) REVERT: B 69 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7838 (mt-10) REVERT: B 126 GLU cc_start: 0.7560 (pm20) cc_final: 0.7067 (mt-10) REVERT: B 157 ASP cc_start: 0.8440 (t0) cc_final: 0.8184 (t0) REVERT: B 181 ASP cc_start: 0.8160 (m-30) cc_final: 0.7947 (m-30) REVERT: B 229 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7954 (mtt-85) REVERT: B 233 GLU cc_start: 0.7323 (tt0) cc_final: 0.6831 (mt-10) REVERT: B 316 GLU cc_start: 0.6911 (tm-30) cc_final: 0.6476 (tm-30) REVERT: B 398 ARG cc_start: 0.7815 (ttm170) cc_final: 0.7238 (tpp-160) REVERT: C 24 MET cc_start: 0.7921 (ptt) cc_final: 0.7553 (ptm) REVERT: C 126 GLU cc_start: 0.7522 (pm20) cc_final: 0.7093 (mt-10) REVERT: C 138 LYS cc_start: 0.8751 (mtpt) cc_final: 0.8494 (ttmm) REVERT: C 233 GLU cc_start: 0.7586 (tt0) cc_final: 0.7136 (mt-10) REVERT: C 303 MET cc_start: 0.8750 (mmt) cc_final: 0.8520 (mmm) REVERT: C 316 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6834 (tm-30) REVERT: C 398 ARG cc_start: 0.7826 (ttm170) cc_final: 0.7308 (tpp-160) REVERT: D 24 MET cc_start: 0.8067 (ptt) cc_final: 0.7693 (ptt) REVERT: D 138 LYS cc_start: 0.8768 (mtpt) cc_final: 0.8503 (mtpp) REVERT: D 157 ASP cc_start: 0.8503 (t0) cc_final: 0.8228 (t70) REVERT: D 235 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7986 (mm-40) REVERT: D 398 ARG cc_start: 0.7828 (ttm170) cc_final: 0.7200 (tpp-160) REVERT: E 72 MET cc_start: 0.8940 (mtm) cc_final: 0.8634 (mtm) REVERT: E 173 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7705 (mt-10) REVERT: E 233 GLU cc_start: 0.7489 (tt0) cc_final: 0.7023 (mt-10) REVERT: E 316 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6704 (tm-30) REVERT: E 398 ARG cc_start: 0.7731 (ttm170) cc_final: 0.7144 (tpp-160) outliers start: 51 outliers final: 25 residues processed: 331 average time/residue: 1.1150 time to fit residues: 407.9783 Evaluate side-chains 289 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 262 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 420 PHE Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 289 SER Chi-restraints excluded: chain E residue 420 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 137 optimal weight: 4.9990 chunk 153 optimal weight: 0.0040 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- 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 62 ASN C 180 ASN D 62 ASN E 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14585 Z= 0.227 Angle : 0.635 6.354 19775 Z= 0.317 Chirality : 0.047 0.162 2265 Planarity : 0.004 0.036 2450 Dihedral : 7.002 34.162 2202 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.94 % Allowed : 17.48 % Favored : 78.58 % 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: -2.80 (0.18), residues: 1710 helix: -2.30 (0.18), residues: 590 sheet: -0.76 (0.30), residues: 320 loop : -1.88 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 422 HIS 0.001 0.000 HIS E 231 PHE 0.010 0.001 PHE C 203 TYR 0.011 0.001 TYR E 144 ARG 0.006 0.000 ARG B 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 351 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 290 time to evaluate : 1.619 Fit side-chains REVERT: A 233 GLU cc_start: 0.7385 (tt0) cc_final: 0.6937 (mt-10) REVERT: A 235 GLN cc_start: 0.8160 (mm110) cc_final: 0.7720 (mm-40) REVERT: A 261 ASN cc_start: 0.7084 (p0) cc_final: 0.6759 (t0) REVERT: A 312 SER cc_start: 0.8276 (m) cc_final: 0.7757 (p) REVERT: A 316 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6547 (tm-30) REVERT: A 325 ARG cc_start: 0.6973 (ttt180) cc_final: 0.6759 (ttp-170) REVERT: A 398 ARG cc_start: 0.7626 (ttm170) cc_final: 0.7023 (tpp-160) REVERT: B 69 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: B 126 GLU cc_start: 0.7461 (pm20) cc_final: 0.6975 (mt-10) REVERT: B 181 ASP cc_start: 0.8219 (m-30) cc_final: 0.8007 (m-30) REVERT: B 316 GLU cc_start: 0.6931 (tm-30) cc_final: 0.6447 (tm-30) REVERT: B 398 ARG cc_start: 0.7723 (ttm170) cc_final: 0.7228 (tpp-160) REVERT: C 138 LYS cc_start: 0.8744 (mtpt) cc_final: 0.8489 (ttmm) REVERT: C 233 GLU cc_start: 0.7526 (tt0) cc_final: 0.7105 (mt-10) REVERT: C 258 PHE cc_start: 0.8908 (m-80) cc_final: 0.8658 (m-80) REVERT: C 312 SER cc_start: 0.8215 (m) cc_final: 0.7846 (p) REVERT: C 316 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6838 (tm-30) REVERT: C 325 ARG cc_start: 0.6951 (ptm-80) cc_final: 0.6746 (ptm-80) REVERT: C 398 ARG cc_start: 0.7768 (ttm170) cc_final: 0.7245 (tpp-160) REVERT: D 24 MET cc_start: 0.8016 (ptt) cc_final: 0.7771 (ptt) REVERT: D 102 ASP cc_start: 0.8262 (t0) cc_final: 0.7758 (t70) REVERT: D 179 MET cc_start: 0.8610 (tpt) cc_final: 0.8224 (tpt) REVERT: D 235 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7979 (mm-40) REVERT: D 398 ARG cc_start: 0.7771 (ttm170) cc_final: 0.7135 (tpp-160) REVERT: E 102 ASP cc_start: 0.8017 (t70) cc_final: 0.7679 (t70) REVERT: E 207 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7979 (tm-30) REVERT: E 233 GLU cc_start: 0.7494 (tt0) cc_final: 0.7002 (mt-10) REVERT: E 235 GLN cc_start: 0.8144 (mm110) cc_final: 0.7738 (mm-40) REVERT: E 316 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6673 (tm-30) REVERT: E 398 ARG cc_start: 0.7635 (ttm170) cc_final: 0.7080 (tpp-160) outliers start: 61 outliers final: 26 residues processed: 322 average time/residue: 0.9720 time to fit residues: 350.6520 Evaluate side-chains 292 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 265 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 420 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 ASN C 62 ASN D 62 ASN E 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14585 Z= 0.286 Angle : 0.625 7.213 19775 Z= 0.315 Chirality : 0.046 0.164 2265 Planarity : 0.003 0.036 2450 Dihedral : 5.873 29.992 2202 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.90 % Allowed : 18.39 % Favored : 76.71 % 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: -2.46 (0.19), residues: 1710 helix: -1.86 (0.19), residues: 620 sheet: -0.39 (0.31), residues: 320 loop : -1.89 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 84 HIS 0.001 0.000 HIS A 125 PHE 0.010 0.001 PHE C 414 TYR 0.011 0.001 TYR D 144 ARG 0.004 0.000 ARG B 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 349 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 273 time to evaluate : 1.610 Fit side-chains REVERT: A 126 GLU cc_start: 0.7344 (pm20) cc_final: 0.6820 (mt-10) REVERT: A 156 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.6800 (mmt) REVERT: A 233 GLU cc_start: 0.7360 (tt0) cc_final: 0.6930 (mt-10) REVERT: A 235 GLN cc_start: 0.8201 (mm110) cc_final: 0.7759 (mm-40) REVERT: A 243 MET cc_start: 0.8521 (mtm) cc_final: 0.8225 (ptp) REVERT: A 312 SER cc_start: 0.8285 (m) cc_final: 0.7787 (p) REVERT: A 316 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6446 (tm-30) REVERT: A 398 ARG cc_start: 0.7632 (ttm170) cc_final: 0.6997 (tpp-160) REVERT: B 69 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: B 181 ASP cc_start: 0.8232 (m-30) cc_final: 0.7984 (m-30) REVERT: B 233 GLU cc_start: 0.7372 (tt0) cc_final: 0.6854 (mt-10) REVERT: B 316 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6521 (tm-30) REVERT: B 398 ARG cc_start: 0.7705 (ttm170) cc_final: 0.7278 (tpp-160) REVERT: C 138 LYS cc_start: 0.8782 (mtpt) cc_final: 0.8557 (ttmm) REVERT: C 233 GLU cc_start: 0.7513 (tt0) cc_final: 0.7087 (mt-10) REVERT: C 312 SER cc_start: 0.8192 (m) cc_final: 0.7839 (p) REVERT: C 316 GLU cc_start: 0.7337 (tm-30) cc_final: 0.6950 (tm-30) REVERT: C 398 ARG cc_start: 0.7788 (ttm170) cc_final: 0.7170 (tpp-160) REVERT: D 102 ASP cc_start: 0.8325 (t0) cc_final: 0.7750 (t70) REVERT: D 156 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7377 (mmt) REVERT: D 235 GLN cc_start: 0.8368 (mm-40) cc_final: 0.8054 (mm-40) REVERT: D 312 SER cc_start: 0.8328 (m) cc_final: 0.7913 (p) REVERT: D 325 ARG cc_start: 0.7188 (ttp-170) cc_final: 0.6948 (ttp-170) REVERT: D 398 ARG cc_start: 0.7748 (ttm170) cc_final: 0.7099 (tpp-160) REVERT: E 102 ASP cc_start: 0.8020 (t70) cc_final: 0.7798 (t70) REVERT: E 156 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7084 (mmt) REVERT: E 233 GLU cc_start: 0.7508 (tt0) cc_final: 0.7020 (mt-10) REVERT: E 235 GLN cc_start: 0.8208 (mm110) cc_final: 0.7804 (mm-40) REVERT: E 261 ASN cc_start: 0.7307 (p0) cc_final: 0.6900 (p0) REVERT: E 316 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6720 (tm-30) REVERT: E 325 ARG cc_start: 0.7084 (ttp-170) cc_final: 0.6870 (ttp-170) REVERT: E 398 ARG cc_start: 0.7567 (ttm170) cc_final: 0.6991 (tpp-160) outliers start: 76 outliers final: 45 residues processed: 310 average time/residue: 1.0170 time to fit residues: 354.1628 Evaluate side-chains 324 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 275 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 56 THR 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 219 ASN Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 420 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 62 ASN D 62 ASN E 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14585 Z= 0.218 Angle : 0.590 7.087 19775 Z= 0.298 Chirality : 0.045 0.161 2265 Planarity : 0.003 0.036 2450 Dihedral : 5.435 25.152 2202 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.39 % Allowed : 19.16 % Favored : 76.45 % 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: -2.12 (0.19), residues: 1710 helix: -1.47 (0.21), residues: 620 sheet: -0.19 (0.31), residues: 320 loop : -1.80 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 84 HIS 0.001 0.000 HIS E 125 PHE 0.009 0.001 PHE D 115 TYR 0.010 0.001 TYR C 144 ARG 0.004 0.000 ARG D 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 287 time to evaluate : 1.668 Fit side-chains REVERT: A 156 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.6577 (mmt) REVERT: A 233 GLU cc_start: 0.7334 (tt0) cc_final: 0.6910 (mt-10) REVERT: A 235 GLN cc_start: 0.8254 (mm110) cc_final: 0.7777 (mm-40) REVERT: A 243 MET cc_start: 0.8516 (mtm) cc_final: 0.8239 (ptp) REVERT: A 312 SER cc_start: 0.8264 (m) cc_final: 0.7782 (p) REVERT: A 316 GLU cc_start: 0.6953 (tm-30) cc_final: 0.6351 (tm-30) REVERT: A 325 ARG cc_start: 0.7224 (ttp-170) cc_final: 0.6972 (ttp-170) REVERT: A 398 ARG cc_start: 0.7613 (ttm170) cc_final: 0.6970 (tpp-160) REVERT: A 419 ILE cc_start: 0.8004 (mm) cc_final: 0.7789 (mt) REVERT: B 69 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: B 181 ASP cc_start: 0.8241 (m-30) cc_final: 0.8006 (m-30) REVERT: B 312 SER cc_start: 0.8205 (m) cc_final: 0.7788 (p) REVERT: B 316 GLU cc_start: 0.7052 (tm-30) cc_final: 0.6536 (tm-30) REVERT: B 398 ARG cc_start: 0.7658 (ttm170) cc_final: 0.7247 (tpp-160) REVERT: C 24 MET cc_start: 0.7360 (ptm) cc_final: 0.7046 (ptm) REVERT: C 138 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8545 (ttmm) REVERT: C 189 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8747 (mttm) REVERT: C 233 GLU cc_start: 0.7476 (tt0) cc_final: 0.7088 (mt-10) REVERT: C 312 SER cc_start: 0.8185 (m) cc_final: 0.7829 (p) REVERT: C 316 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6863 (tm-30) REVERT: C 398 ARG cc_start: 0.7777 (ttm170) cc_final: 0.7086 (tpp-160) REVERT: D 102 ASP cc_start: 0.8293 (t0) cc_final: 0.7706 (t70) REVERT: D 235 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8094 (mm-40) REVERT: D 312 SER cc_start: 0.8288 (m) cc_final: 0.7863 (p) REVERT: D 398 ARG cc_start: 0.7748 (ttm170) cc_final: 0.7085 (tpp-160) REVERT: E 102 ASP cc_start: 0.8020 (t70) cc_final: 0.7777 (t70) REVERT: E 233 GLU cc_start: 0.7486 (tt0) cc_final: 0.7003 (mt-10) REVERT: E 235 GLN cc_start: 0.8239 (mm110) cc_final: 0.7841 (mm-40) REVERT: E 290 LEU cc_start: 0.9172 (mm) cc_final: 0.8967 (mt) REVERT: E 312 SER cc_start: 0.8056 (m) cc_final: 0.7631 (p) REVERT: E 316 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6697 (tm-30) REVERT: E 325 ARG cc_start: 0.7066 (ttp-170) cc_final: 0.6801 (ttp-170) REVERT: E 398 ARG cc_start: 0.7521 (ttm170) cc_final: 0.6919 (tpp-160) outliers start: 68 outliers final: 37 residues processed: 317 average time/residue: 1.0520 time to fit residues: 371.3511 Evaluate side-chains 303 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 264 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 281 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 62 ASN C 62 ASN D 62 ASN E 62 ASN E 123 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14585 Z= 0.200 Angle : 0.580 8.702 19775 Z= 0.294 Chirality : 0.044 0.162 2265 Planarity : 0.003 0.036 2450 Dihedral : 5.204 24.058 2200 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.65 % Allowed : 19.81 % Favored : 75.55 % 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: -1.82 (0.20), residues: 1710 helix: -1.14 (0.21), residues: 620 sheet: -0.01 (0.31), residues: 320 loop : -1.72 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 84 HIS 0.001 0.000 HIS A 125 PHE 0.009 0.001 PHE C 115 TYR 0.010 0.001 TYR C 144 ARG 0.007 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 347 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 275 time to evaluate : 1.648 Fit side-chains REVERT: A 233 GLU cc_start: 0.7276 (tt0) cc_final: 0.6851 (mt-10) REVERT: A 235 GLN cc_start: 0.8276 (mm110) cc_final: 0.7797 (mm-40) REVERT: A 243 MET cc_start: 0.8520 (mtm) cc_final: 0.8221 (ptp) REVERT: A 312 SER cc_start: 0.8278 (m) cc_final: 0.7790 (p) REVERT: A 316 GLU cc_start: 0.6958 (tm-30) cc_final: 0.6344 (tm-30) REVERT: A 325 ARG cc_start: 0.7263 (ttp-170) cc_final: 0.7004 (ttp-170) REVERT: A 398 ARG cc_start: 0.7554 (ttm170) cc_final: 0.6846 (tpp-160) REVERT: B 69 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: B 181 ASP cc_start: 0.8256 (m-30) cc_final: 0.8024 (m-30) REVERT: B 312 SER cc_start: 0.8243 (m) cc_final: 0.7831 (p) REVERT: B 316 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6525 (tm-30) REVERT: B 398 ARG cc_start: 0.7627 (ttm170) cc_final: 0.7160 (tpp-160) REVERT: C 24 MET cc_start: 0.7389 (ptm) cc_final: 0.7181 (ptm) REVERT: C 102 ASP cc_start: 0.8421 (t0) cc_final: 0.7950 (t70) REVERT: C 138 LYS cc_start: 0.8772 (mtpt) cc_final: 0.8546 (ttmm) REVERT: C 189 LYS cc_start: 0.9065 (mtmm) cc_final: 0.8757 (mttm) REVERT: C 233 GLU cc_start: 0.7459 (tt0) cc_final: 0.7075 (mt-10) REVERT: C 312 SER cc_start: 0.8201 (m) cc_final: 0.7851 (p) REVERT: C 316 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6840 (tm-30) REVERT: C 398 ARG cc_start: 0.7758 (ttm170) cc_final: 0.7086 (tpp-160) REVERT: D 28 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8471 (tt0) REVERT: D 102 ASP cc_start: 0.8306 (t0) cc_final: 0.7604 (t70) REVERT: D 179 MET cc_start: 0.8639 (tpt) cc_final: 0.8119 (tpt) REVERT: D 235 GLN cc_start: 0.8407 (mm-40) cc_final: 0.8108 (mm-40) REVERT: D 312 SER cc_start: 0.8259 (m) cc_final: 0.7838 (p) REVERT: D 325 ARG cc_start: 0.7177 (ttp-170) cc_final: 0.6877 (ttp-170) REVERT: D 398 ARG cc_start: 0.7752 (ttm170) cc_final: 0.7001 (tpp-160) REVERT: E 24 MET cc_start: 0.7615 (ptm) cc_final: 0.7297 (ptp) REVERT: E 69 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: E 102 ASP cc_start: 0.8020 (t70) cc_final: 0.7637 (t70) REVERT: E 208 GLU cc_start: 0.8080 (tp30) cc_final: 0.7595 (pt0) REVERT: E 233 GLU cc_start: 0.7489 (tt0) cc_final: 0.7018 (mt-10) REVERT: E 235 GLN cc_start: 0.8271 (mm110) cc_final: 0.7881 (mm-40) REVERT: E 290 LEU cc_start: 0.9163 (mm) cc_final: 0.8934 (mt) REVERT: E 312 SER cc_start: 0.8046 (m) cc_final: 0.7622 (p) REVERT: E 316 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6779 (tm-30) REVERT: E 325 ARG cc_start: 0.7025 (ttp-170) cc_final: 0.6465 (ttt180) REVERT: E 398 ARG cc_start: 0.7488 (ttm170) cc_final: 0.6875 (tpp-160) outliers start: 72 outliers final: 44 residues processed: 309 average time/residue: 1.0448 time to fit residues: 359.0715 Evaluate side-chains 318 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 272 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 281 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 62 ASN D 62 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14585 Z= 0.313 Angle : 0.629 8.580 19775 Z= 0.317 Chirality : 0.046 0.167 2265 Planarity : 0.003 0.035 2450 Dihedral : 5.293 26.602 2200 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.45 % Allowed : 21.29 % Favored : 74.26 % 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: -1.67 (0.20), residues: 1710 helix: -1.02 (0.21), residues: 625 sheet: 0.01 (0.31), residues: 325 loop : -1.60 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 302 HIS 0.001 0.000 HIS E 125 PHE 0.011 0.001 PHE D 115 TYR 0.012 0.001 TYR D 144 ARG 0.007 0.000 ARG B 325 *********************** 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 336 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 267 time to evaluate : 1.737 Fit side-chains REVERT: A 207 GLU cc_start: 0.7931 (tt0) cc_final: 0.7625 (tm-30) REVERT: A 233 GLU cc_start: 0.7376 (tt0) cc_final: 0.6947 (mt-10) REVERT: A 235 GLN cc_start: 0.8276 (mm110) cc_final: 0.7818 (mm-40) REVERT: A 243 MET cc_start: 0.8545 (mtm) cc_final: 0.8209 (ptp) REVERT: A 312 SER cc_start: 0.8296 (m) cc_final: 0.7802 (p) REVERT: A 316 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6460 (tm-30) REVERT: A 325 ARG cc_start: 0.7226 (ttp-170) cc_final: 0.6944 (ttp-170) REVERT: A 398 ARG cc_start: 0.7592 (ttm170) cc_final: 0.6832 (tpp-160) REVERT: B 69 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7914 (mt-10) REVERT: B 156 MET cc_start: 0.8426 (mmt) cc_final: 0.7966 (mmt) REVERT: B 312 SER cc_start: 0.8248 (m) cc_final: 0.7832 (p) REVERT: B 316 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6622 (tm-30) REVERT: B 398 ARG cc_start: 0.7639 (ttm170) cc_final: 0.7126 (tpp-160) REVERT: C 102 ASP cc_start: 0.8452 (t0) cc_final: 0.7971 (t70) REVERT: C 138 LYS cc_start: 0.8810 (mtpt) cc_final: 0.8520 (ttmt) REVERT: C 189 LYS cc_start: 0.9066 (mtmm) cc_final: 0.8752 (mttm) REVERT: C 233 GLU cc_start: 0.7470 (tt0) cc_final: 0.7055 (mt-10) REVERT: C 312 SER cc_start: 0.8225 (m) cc_final: 0.7870 (p) REVERT: C 316 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6939 (tm-30) REVERT: C 398 ARG cc_start: 0.7786 (ttm170) cc_final: 0.7086 (tpp-160) REVERT: D 102 ASP cc_start: 0.8421 (t0) cc_final: 0.7830 (t70) REVERT: D 156 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.7292 (mmt) REVERT: D 235 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8155 (mm-40) REVERT: D 312 SER cc_start: 0.8305 (m) cc_final: 0.7906 (p) REVERT: D 398 ARG cc_start: 0.7743 (ttm170) cc_final: 0.6991 (tpp-160) REVERT: E 69 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: E 102 ASP cc_start: 0.8165 (t70) cc_final: 0.7797 (t70) REVERT: E 156 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.7394 (mmt) REVERT: E 233 GLU cc_start: 0.7527 (tt0) cc_final: 0.7028 (mt-10) REVERT: E 235 GLN cc_start: 0.8283 (mm110) cc_final: 0.7893 (mm-40) REVERT: E 290 LEU cc_start: 0.9196 (mm) cc_final: 0.8970 (mt) REVERT: E 312 SER cc_start: 0.8077 (m) cc_final: 0.7650 (p) REVERT: E 316 GLU cc_start: 0.7330 (tm-30) cc_final: 0.6769 (tm-30) REVERT: E 325 ARG cc_start: 0.6973 (ttp-170) cc_final: 0.6422 (ttt180) REVERT: E 398 ARG cc_start: 0.7542 (ttm170) cc_final: 0.6870 (tpp-160) outliers start: 69 outliers final: 48 residues processed: 298 average time/residue: 1.0324 time to fit residues: 342.8175 Evaluate side-chains 317 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 265 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 56 THR 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 219 ASN Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 163 MET Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 281 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 111 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 62 ASN ** E 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14585 Z= 0.240 Angle : 0.606 10.123 19775 Z= 0.305 Chirality : 0.045 0.165 2265 Planarity : 0.003 0.039 2450 Dihedral : 5.231 26.405 2200 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.19 % Allowed : 22.32 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.20), residues: 1710 helix: -0.84 (0.22), residues: 625 sheet: 0.17 (0.31), residues: 320 loop : -1.56 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 186 HIS 0.001 0.000 HIS E 125 PHE 0.010 0.001 PHE D 258 TYR 0.011 0.001 TYR D 317 ARG 0.005 0.000 ARG B 325 *********************** 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 336 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 271 time to evaluate : 1.561 Fit side-chains REVERT: A 233 GLU cc_start: 0.7311 (tt0) cc_final: 0.6874 (mt-10) REVERT: A 235 GLN cc_start: 0.8277 (mm110) cc_final: 0.7821 (mm-40) REVERT: A 243 MET cc_start: 0.8512 (mtm) cc_final: 0.8200 (ptp) REVERT: A 312 SER cc_start: 0.8279 (m) cc_final: 0.7784 (p) REVERT: A 316 GLU cc_start: 0.7043 (tm-30) cc_final: 0.6391 (tm-30) REVERT: A 398 ARG cc_start: 0.7596 (ttm170) cc_final: 0.6806 (tpp-160) REVERT: B 69 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: B 312 SER cc_start: 0.8204 (m) cc_final: 0.7794 (p) REVERT: B 316 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6597 (tm-30) REVERT: B 325 ARG cc_start: 0.7629 (ttp-170) cc_final: 0.7203 (ttp-170) REVERT: B 398 ARG cc_start: 0.7625 (ttm170) cc_final: 0.7122 (tpp-160) REVERT: C 102 ASP cc_start: 0.8461 (t0) cc_final: 0.7972 (t70) REVERT: C 138 LYS cc_start: 0.8803 (mtpt) cc_final: 0.8507 (ttmt) REVERT: C 233 GLU cc_start: 0.7420 (tt0) cc_final: 0.7002 (mt-10) REVERT: C 312 SER cc_start: 0.8205 (m) cc_final: 0.7850 (p) REVERT: C 316 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6889 (tm-30) REVERT: C 398 ARG cc_start: 0.7772 (ttm170) cc_final: 0.7034 (tpp-160) REVERT: D 102 ASP cc_start: 0.8395 (t0) cc_final: 0.7967 (t70) REVERT: D 156 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.7196 (mmt) REVERT: D 235 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8155 (mm-40) REVERT: D 312 SER cc_start: 0.8125 (m) cc_final: 0.7730 (p) REVERT: D 325 ARG cc_start: 0.7426 (ttp-170) cc_final: 0.7158 (ttp-170) REVERT: D 398 ARG cc_start: 0.7751 (ttm170) cc_final: 0.7004 (tpp-160) REVERT: E 69 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7917 (mt-10) REVERT: E 156 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7442 (mmt) REVERT: E 181 ASP cc_start: 0.8316 (m-30) cc_final: 0.8101 (m-30) REVERT: E 208 GLU cc_start: 0.8046 (tp30) cc_final: 0.7628 (pt0) REVERT: E 227 GLU cc_start: 0.8449 (pt0) cc_final: 0.8113 (pt0) REVERT: E 233 GLU cc_start: 0.7502 (tt0) cc_final: 0.7013 (mt-10) REVERT: E 235 GLN cc_start: 0.8281 (mm110) cc_final: 0.7889 (mm-40) REVERT: E 290 LEU cc_start: 0.9173 (mm) cc_final: 0.8937 (mt) REVERT: E 312 SER cc_start: 0.8041 (m) cc_final: 0.7611 (p) REVERT: E 316 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6596 (tm-30) REVERT: E 398 ARG cc_start: 0.7519 (ttm170) cc_final: 0.6804 (tpp-160) outliers start: 65 outliers final: 47 residues processed: 300 average time/residue: 0.9912 time to fit residues: 332.7877 Evaluate side-chains 315 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 264 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 27 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 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 37 VAL 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 163 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 281 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 66 optimal weight: 0.0980 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 144 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 161 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 180 ASN B 62 ASN C 62 ASN C 180 ASN E 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14585 Z= 0.181 Angle : 0.580 9.888 19775 Z= 0.290 Chirality : 0.044 0.178 2265 Planarity : 0.003 0.034 2450 Dihedral : 5.037 23.565 2200 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.74 % Allowed : 23.03 % Favored : 73.23 % 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: -1.35 (0.20), residues: 1710 helix: -0.53 (0.22), residues: 610 sheet: 0.20 (0.30), residues: 320 loop : -1.63 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 186 HIS 0.001 0.000 HIS E 125 PHE 0.009 0.001 PHE D 115 TYR 0.010 0.001 TYR D 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 333 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 275 time to evaluate : 1.685 Fit side-chains REVERT: A 233 GLU cc_start: 0.7305 (tt0) cc_final: 0.6907 (mt-10) REVERT: A 235 GLN cc_start: 0.8286 (mm110) cc_final: 0.7796 (mm-40) REVERT: A 243 MET cc_start: 0.8475 (mtm) cc_final: 0.8237 (ptp) REVERT: A 312 SER cc_start: 0.8250 (m) cc_final: 0.7773 (p) REVERT: A 316 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6330 (tm-30) REVERT: A 398 ARG cc_start: 0.7575 (ttm170) cc_final: 0.6827 (tpp-160) REVERT: B 69 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: B 312 SER cc_start: 0.8206 (m) cc_final: 0.7791 (p) REVERT: B 316 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6634 (tm-30) REVERT: B 398 ARG cc_start: 0.7620 (ttm170) cc_final: 0.7089 (tpp-160) REVERT: C 138 LYS cc_start: 0.8790 (mtpt) cc_final: 0.8497 (ttmt) REVERT: C 233 GLU cc_start: 0.7325 (tt0) cc_final: 0.6955 (mt-10) REVERT: C 312 SER cc_start: 0.8202 (m) cc_final: 0.7839 (p) REVERT: C 316 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6819 (tm-30) REVERT: C 398 ARG cc_start: 0.7751 (ttm170) cc_final: 0.7038 (tpp-160) REVERT: D 179 MET cc_start: 0.8609 (tpt) cc_final: 0.8046 (tpt) REVERT: D 235 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8172 (mm-40) REVERT: D 325 ARG cc_start: 0.7458 (ttp-170) cc_final: 0.7224 (ttp-170) REVERT: D 398 ARG cc_start: 0.7733 (ttm170) cc_final: 0.6987 (tpp-160) REVERT: E 69 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: E 102 ASP cc_start: 0.8416 (t70) cc_final: 0.7732 (t70) REVERT: E 156 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7455 (mmt) REVERT: E 208 GLU cc_start: 0.8020 (tp30) cc_final: 0.7509 (pt0) REVERT: E 227 GLU cc_start: 0.8372 (pt0) cc_final: 0.8006 (pt0) REVERT: E 233 GLU cc_start: 0.7448 (tt0) cc_final: 0.6991 (mt-10) REVERT: E 235 GLN cc_start: 0.8294 (mm110) cc_final: 0.7903 (mm-40) REVERT: E 290 LEU cc_start: 0.9154 (mm) cc_final: 0.8935 (mt) REVERT: E 312 SER cc_start: 0.8030 (m) cc_final: 0.7593 (p) REVERT: E 316 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6640 (tm-30) REVERT: E 325 ARG cc_start: 0.6831 (ttp-170) cc_final: 0.6614 (ttp-170) REVERT: E 398 ARG cc_start: 0.7536 (ttm170) cc_final: 0.6817 (tpp-160) outliers start: 58 outliers final: 38 residues processed: 300 average time/residue: 1.0182 time to fit residues: 340.6381 Evaluate side-chains 306 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 265 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain D residue 27 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 281 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.1980 chunk 76 optimal weight: 0.0570 chunk 112 optimal weight: 4.9990 chunk 169 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 134 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 82 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.2096 ------------------------------------------------------------------------------- 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 62 ASN C 180 ASN D 62 ASN E 62 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14585 Z= 0.146 Angle : 0.579 10.337 19775 Z= 0.289 Chirality : 0.044 0.186 2265 Planarity : 0.003 0.034 2450 Dihedral : 4.888 21.305 2200 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.03 % Allowed : 24.06 % Favored : 72.90 % 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: -1.26 (0.20), residues: 1710 helix: -0.41 (0.22), residues: 610 sheet: 0.25 (0.30), residues: 320 loop : -1.62 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 84 HIS 0.001 0.000 HIS E 125 PHE 0.011 0.001 PHE C 417 TYR 0.009 0.001 TYR A 295 ARG 0.008 0.000 ARG A 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 275 time to evaluate : 1.430 Fit side-chains REVERT: A 58 ASN cc_start: 0.7852 (p0) cc_final: 0.7643 (p0) REVERT: A 233 GLU cc_start: 0.7200 (tt0) cc_final: 0.6846 (mt-10) REVERT: A 235 GLN cc_start: 0.8274 (mm110) cc_final: 0.7754 (mm-40) REVERT: A 243 MET cc_start: 0.8452 (mtm) cc_final: 0.8205 (ptp) REVERT: A 312 SER cc_start: 0.8234 (m) cc_final: 0.7763 (p) REVERT: A 316 GLU cc_start: 0.6921 (tm-30) cc_final: 0.6241 (tm-30) REVERT: A 325 ARG cc_start: 0.7406 (ttp-170) cc_final: 0.7139 (ttp-170) REVERT: A 398 ARG cc_start: 0.7556 (ttm170) cc_final: 0.6812 (tpp-160) REVERT: B 69 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: B 71 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.9037 (p) REVERT: B 208 GLU cc_start: 0.8062 (tp30) cc_final: 0.7654 (pt0) REVERT: B 312 SER cc_start: 0.8209 (m) cc_final: 0.7805 (p) REVERT: B 316 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6532 (tm-30) REVERT: B 325 ARG cc_start: 0.7345 (ttp-170) cc_final: 0.6904 (ttp-170) REVERT: B 398 ARG cc_start: 0.7607 (ttm170) cc_final: 0.7079 (tpp-160) REVERT: C 102 ASP cc_start: 0.8527 (t70) cc_final: 0.8015 (t70) REVERT: C 138 LYS cc_start: 0.8791 (mtpt) cc_final: 0.8541 (ttmm) REVERT: C 233 GLU cc_start: 0.7223 (tt0) cc_final: 0.6928 (mt-10) REVERT: C 235 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8261 (mm-40) REVERT: C 312 SER cc_start: 0.8179 (m) cc_final: 0.7819 (p) REVERT: C 316 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6696 (tm-30) REVERT: C 398 ARG cc_start: 0.7679 (ttm170) cc_final: 0.6934 (tpp-160) REVERT: D 28 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8395 (tt0) REVERT: D 102 ASP cc_start: 0.8432 (t70) cc_final: 0.7878 (t70) REVERT: D 156 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7107 (mmt) REVERT: D 233 GLU cc_start: 0.7126 (tt0) cc_final: 0.6707 (mt-10) REVERT: D 235 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8166 (mm-40) REVERT: D 325 ARG cc_start: 0.7470 (ttp-170) cc_final: 0.7242 (ttp-170) REVERT: D 398 ARG cc_start: 0.7709 (ttm170) cc_final: 0.6968 (tpp-160) REVERT: E 69 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: E 102 ASP cc_start: 0.8408 (t70) cc_final: 0.7892 (t70) REVERT: E 156 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.7461 (mmt) REVERT: E 208 GLU cc_start: 0.8027 (tp30) cc_final: 0.7506 (pt0) REVERT: E 233 GLU cc_start: 0.7379 (tt0) cc_final: 0.6957 (mt-10) REVERT: E 235 GLN cc_start: 0.8322 (mm110) cc_final: 0.7934 (mm-40) REVERT: E 316 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6548 (tm-30) REVERT: E 398 ARG cc_start: 0.7505 (ttm170) cc_final: 0.6785 (tpp-160) outliers start: 47 outliers final: 30 residues processed: 296 average time/residue: 1.0737 time to fit residues: 352.1230 Evaluate side-chains 309 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 274 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 189 LYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 156 MET Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 420 PHE Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 69 GLU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 281 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 chunk 19 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 138 optimal weight: 0.0070 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 118 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 62 ASN C 62 ASN C 180 ASN D 62 ASN E 62 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.149139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.113776 restraints weight = 16801.166| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.40 r_work: 0.3101 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14585 Z= 0.163 Angle : 0.578 10.123 19775 Z= 0.288 Chirality : 0.044 0.171 2265 Planarity : 0.003 0.029 2450 Dihedral : 4.817 21.282 2200 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.58 % Allowed : 24.65 % Favored : 72.77 % 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: -1.19 (0.20), residues: 1710 helix: -0.39 (0.22), residues: 615 sheet: 0.35 (0.30), residues: 320 loop : -1.58 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 186 HIS 0.001 0.000 HIS E 125 PHE 0.013 0.001 PHE B 258 TYR 0.009 0.001 TYR E 144 ARG 0.008 0.000 ARG A 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5975.86 seconds wall clock time: 105 minutes 47.55 seconds (6347.55 seconds total)