Starting phenix.real_space_refine on Fri Feb 16 03:18:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6m_23700/02_2024/7m6m_23700_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6m_23700/02_2024/7m6m_23700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6m_23700/02_2024/7m6m_23700.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6m_23700/02_2024/7m6m_23700.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6m_23700/02_2024/7m6m_23700_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6m_23700/02_2024/7m6m_23700_updated.pdb" } resolution = 3.09 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= 0.003 sd= 0.041 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 95 5.16 5 C 9275 2.51 5 N 2275 2.21 5 O 2545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14190 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2787 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 16, 'TRANS': 327} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2787 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 16, 'TRANS': 327} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2787 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 16, 'TRANS': 327} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2787 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 16, 'TRANS': 327} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2787 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 16, 'TRANS': 327} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'TCI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'TCI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'TCI': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'TCI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'TCI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.94, per 1000 atoms: 0.56 Number of scatterers: 14190 At special positions: 0 Unit cell: (100.7, 100.7, 132.5, 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 95 16.00 O 2545 8.00 N 2275 7.00 C 9275 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG F 1 " - " ASN A 62 " " NAG G 1 " - " ASN B 62 " " NAG H 1 " - " ASN C 62 " " NAG I 1 " - " ASN E 62 " " NAG J 1 " - " ASN D 62 " Time building additional restraints: 5.60 Conformation dependent library (CDL) restraints added in 2.7 seconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 25 sheets defined 34.0% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 34 through 42 removed outlier: 3.519A pdb=" N LEU A 38 " --> pdb=" O PRO A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 Processing helix chain 'A' and resid 252 through 267 removed outlier: 3.631A pdb=" N VAL A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N PHE A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP A 267 " --> pdb=" O TRP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 297 removed outlier: 4.203A pdb=" N ALA A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 328 removed outlier: 3.580A pdb=" N TYR A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 440 Proline residue: A 419 - end of helix Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.518A pdb=" N LEU B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 Processing helix chain 'B' and resid 252 through 267 removed outlier: 3.631A pdb=" N VAL B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N SER B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N PHE B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP B 267 " --> pdb=" O TRP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 297 removed outlier: 4.202A pdb=" N ALA B 296 " --> pdb=" O SER B 292 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER B 297 " --> pdb=" O GLY B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 328 removed outlier: 3.579A pdb=" N TYR B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 440 Proline residue: B 419 - end of helix Processing helix chain 'C' and resid 34 through 42 removed outlier: 3.518A pdb=" N LEU C 38 " --> pdb=" O PRO C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 249 Processing helix chain 'C' and resid 252 through 267 removed outlier: 3.631A pdb=" N VAL C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N PHE C 266 " --> pdb=" O SER C 262 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TRP C 267 " --> pdb=" O TRP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 297 removed outlier: 4.202A pdb=" N ALA C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER C 297 " --> pdb=" O GLY C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 328 removed outlier: 3.579A pdb=" N TYR C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 440 Proline residue: C 419 - end of helix Processing helix chain 'E' and resid 34 through 42 removed outlier: 3.518A pdb=" N LEU E 38 " --> pdb=" O PRO E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 252 through 267 removed outlier: 3.630A pdb=" N VAL E 264 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N PHE E 266 " --> pdb=" O SER E 262 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP E 267 " --> pdb=" O TRP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 297 removed outlier: 4.203A pdb=" N ALA E 296 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER E 297 " --> pdb=" O GLY E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 328 removed outlier: 3.579A pdb=" N TYR E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 440 Proline residue: E 419 - end of helix Processing helix chain 'D' and resid 34 through 42 removed outlier: 3.519A pdb=" N LEU D 38 " --> pdb=" O PRO D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 249 Processing helix chain 'D' and resid 252 through 267 removed outlier: 3.630A pdb=" N VAL D 264 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N PHE D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TRP D 267 " --> pdb=" O TRP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 297 removed outlier: 4.203A pdb=" N ALA D 296 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER D 297 " --> pdb=" O GLY D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 328 removed outlier: 3.579A pdb=" N TYR D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 440 Proline residue: D 419 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 190 through 194 removed outlier: 5.672A pdb=" N VAL A 61 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU A 193 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 68 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU A 142 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 67 through 69 Processing sheet with id= C, first strand: chain 'A' and resid 122 through 124 Processing sheet with id= D, first strand: chain 'A' and resid 219 through 225 Processing sheet with id= E, first strand: chain 'A' and resid 127 through 132 removed outlier: 6.810A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 190 through 194 removed outlier: 5.672A pdb=" N VAL B 61 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU B 193 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 68 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU B 142 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 67 through 69 Processing sheet with id= H, first strand: chain 'B' and resid 122 through 124 Processing sheet with id= I, first strand: chain 'B' and resid 219 through 225 Processing sheet with id= J, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.811A pdb=" N VAL B 159 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 190 through 194 removed outlier: 5.672A pdb=" N VAL C 61 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU C 193 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 68 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU C 142 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 67 through 69 Processing sheet with id= M, first strand: chain 'C' and resid 122 through 124 Processing sheet with id= N, first strand: chain 'C' and resid 219 through 225 Processing sheet with id= O, first strand: chain 'C' and resid 127 through 132 removed outlier: 6.810A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 190 through 194 removed outlier: 5.672A pdb=" N VAL E 61 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU E 193 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE E 68 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU E 142 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 67 through 69 Processing sheet with id= R, first strand: chain 'E' and resid 122 through 124 Processing sheet with id= S, first strand: chain 'E' and resid 219 through 225 Processing sheet with id= T, first strand: chain 'E' and resid 127 through 132 removed outlier: 6.811A pdb=" N VAL E 159 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA E 130 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR E 157 " --> pdb=" O ALA E 130 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 190 through 194 removed outlier: 5.672A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE D 68 " --> pdb=" O PHE D 87 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU D 142 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 67 through 69 Processing sheet with id= W, first strand: chain 'D' and resid 122 through 124 Processing sheet with id= X, first strand: chain 'D' and resid 219 through 225 Processing sheet with id= Y, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.810A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) 645 hydrogen bonds defined for protein. 1935 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: 4.37 Time building geometry restraints manager: 6.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4010 1.34 - 1.46: 3081 1.46 - 1.57: 7294 1.57 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 14545 Sorted by residual: bond pdb=" CB MET D 244 " pdb=" CG MET D 244 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.63e+00 bond pdb=" CB MET A 244 " pdb=" CG MET A 244 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.60e+00 bond pdb=" CB MET C 244 " pdb=" CG MET C 244 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.56e+00 bond pdb=" CB MET E 244 " pdb=" CG MET E 244 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.55e+00 bond pdb=" CB MET B 244 " pdb=" CG MET B 244 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.49e+00 ... (remaining 14540 not shown) Histogram of bond angle deviations from ideal: 99.90 - 106.75: 595 106.75 - 113.60: 7554 113.60 - 120.45: 5830 120.45 - 127.30: 5591 127.30 - 134.15: 175 Bond angle restraints: 19745 Sorted by residual: angle pdb=" N PHE A 418 " pdb=" CA PHE A 418 " pdb=" C PHE A 418 " ideal model delta sigma weight residual 112.75 118.16 -5.41 1.36e+00 5.41e-01 1.58e+01 angle pdb=" N PHE B 418 " pdb=" CA PHE B 418 " pdb=" C PHE B 418 " ideal model delta sigma weight residual 112.75 118.14 -5.39 1.36e+00 5.41e-01 1.57e+01 angle pdb=" N PHE D 418 " pdb=" CA PHE D 418 " pdb=" C PHE D 418 " ideal model delta sigma weight residual 112.75 118.13 -5.38 1.36e+00 5.41e-01 1.56e+01 angle pdb=" N PHE E 418 " pdb=" CA PHE E 418 " pdb=" C PHE E 418 " ideal model delta sigma weight residual 112.75 118.12 -5.37 1.36e+00 5.41e-01 1.56e+01 angle pdb=" N PHE C 418 " pdb=" CA PHE C 418 " pdb=" C PHE C 418 " ideal model delta sigma weight residual 112.75 118.11 -5.36 1.36e+00 5.41e-01 1.55e+01 ... (remaining 19740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 8215 16.26 - 32.52: 515 32.52 - 48.79: 105 48.79 - 65.05: 30 65.05 - 81.31: 10 Dihedral angle restraints: 8875 sinusoidal: 3790 harmonic: 5085 Sorted by residual: dihedral pdb=" CA TYR E 221 " pdb=" C TYR E 221 " pdb=" N CYS E 222 " pdb=" CA CYS E 222 " ideal model delta harmonic sigma weight residual 180.00 161.65 18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR B 221 " pdb=" C TYR B 221 " pdb=" N CYS B 222 " pdb=" CA CYS B 222 " ideal model delta harmonic sigma weight residual 180.00 161.68 18.32 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA TYR C 221 " pdb=" C TYR C 221 " pdb=" N CYS C 222 " pdb=" CA CYS C 222 " ideal model delta harmonic sigma weight residual 180.00 161.69 18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 8872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1510 0.064 - 0.129: 459 0.129 - 0.193: 206 0.193 - 0.258: 46 0.258 - 0.322: 19 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA PHE B 418 " pdb=" N PHE B 418 " pdb=" C PHE B 418 " pdb=" CB PHE B 418 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA PHE A 418 " pdb=" N PHE A 418 " pdb=" C PHE A 418 " pdb=" CB PHE A 418 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA PHE C 418 " pdb=" N PHE C 418 " pdb=" C PHE C 418 " pdb=" CB PHE C 418 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 2237 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 247 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C TYR E 247 " 0.060 2.00e-02 2.50e+03 pdb=" O TYR E 247 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU E 248 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 247 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C TYR B 247 " 0.060 2.00e-02 2.50e+03 pdb=" O TYR B 247 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU B 248 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 247 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C TYR A 247 " 0.060 2.00e-02 2.50e+03 pdb=" O TYR A 247 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU A 248 " -0.020 2.00e-02 2.50e+03 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 5128 2.89 - 3.39: 13214 3.39 - 3.89: 23132 3.89 - 4.40: 25209 4.40 - 4.90: 44841 Nonbonded interactions: 111524 Sorted by model distance: nonbonded pdb=" OD2 ASP B 49 " pdb=" OG SER C 35 " model vdw 2.383 2.440 nonbonded pdb=" O LEU E 298 " pdb=" NZ LYS E 300 " model vdw 2.401 2.520 nonbonded pdb=" O LEU A 298 " pdb=" NZ LYS A 300 " model vdw 2.401 2.520 nonbonded pdb=" O LEU D 298 " pdb=" NZ LYS D 300 " model vdw 2.402 2.520 nonbonded pdb=" O LEU C 298 " pdb=" NZ LYS C 300 " model vdw 2.402 2.520 ... (remaining 111519 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=0.57 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: 1.320 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: 0.020 Extract box with map and model: 6.170 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 40.690 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.120 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.008 0.072 14545 Z= 0.529 Angle : 1.312 10.359 19745 Z= 0.728 Chirality : 0.080 0.322 2240 Planarity : 0.008 0.056 2435 Dihedral : 11.549 81.309 5575 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: 0.33 (0.20), residues: 1700 helix: 1.66 (0.20), residues: 570 sheet: 0.66 (0.27), residues: 420 loop : -1.30 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 263 HIS 0.003 0.001 HIS A 133 PHE 0.041 0.004 PHE A 192 TYR 0.029 0.004 TYR C 152 ARG 0.008 0.001 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 543 time to evaluate : 1.705 Fit side-chains revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8297 (t80) cc_final: 0.7985 (t80) REVERT: A 66 ASN cc_start: 0.8278 (m-40) cc_final: 0.7856 (m-40) REVERT: A 89 ARG cc_start: 0.8138 (ttt-90) cc_final: 0.7781 (ttt-90) REVERT: A 141 LEU cc_start: 0.8725 (tp) cc_final: 0.8439 (tt) REVERT: A 143 ARG cc_start: 0.8533 (ttp-110) cc_final: 0.8236 (ttm-80) REVERT: A 193 GLU cc_start: 0.8628 (pm20) cc_final: 0.8004 (pm20) REVERT: A 235 GLU cc_start: 0.7665 (tt0) cc_final: 0.7433 (tt0) REVERT: A 249 ILE cc_start: 0.8725 (tt) cc_final: 0.8418 (tp) REVERT: A 292 SER cc_start: 0.8869 (m) cc_final: 0.8561 (p) REVERT: A 402 LEU cc_start: 0.8630 (mt) cc_final: 0.8398 (pp) REVERT: B 37 PHE cc_start: 0.8268 (t80) cc_final: 0.7785 (t80) REVERT: B 49 ASP cc_start: 0.7713 (t0) cc_final: 0.7481 (t0) REVERT: B 121 ASP cc_start: 0.8580 (p0) cc_final: 0.8345 (p0) REVERT: B 141 LEU cc_start: 0.8644 (tp) cc_final: 0.8375 (tt) REVERT: B 143 ARG cc_start: 0.8474 (ttp-110) cc_final: 0.7958 (ttm-80) REVERT: B 218 ASP cc_start: 0.8755 (p0) cc_final: 0.8408 (p0) REVERT: B 263 TRP cc_start: 0.8281 (m-10) cc_final: 0.8063 (m-10) REVERT: B 300 LYS cc_start: 0.7801 (mmtm) cc_final: 0.7497 (mptt) REVERT: B 402 LEU cc_start: 0.8755 (mt) cc_final: 0.8457 (pp) REVERT: C 37 PHE cc_start: 0.8325 (t80) cc_final: 0.8085 (t80) REVERT: C 143 ARG cc_start: 0.8424 (ttp-110) cc_final: 0.8124 (ttm-80) REVERT: C 179 GLN cc_start: 0.8602 (pt0) cc_final: 0.8385 (pt0) REVERT: C 311 MET cc_start: 0.8695 (mmt) cc_final: 0.8494 (mmm) REVERT: C 402 LEU cc_start: 0.8577 (mt) cc_final: 0.8318 (pp) REVERT: E 38 LEU cc_start: 0.8802 (mt) cc_final: 0.8573 (mm) REVERT: E 49 ASP cc_start: 0.7827 (t0) cc_final: 0.7575 (t0) REVERT: E 121 ASP cc_start: 0.8537 (p0) cc_final: 0.8073 (p0) REVERT: E 143 ARG cc_start: 0.8482 (ttp-110) cc_final: 0.8274 (ttm-80) REVERT: E 179 GLN cc_start: 0.8702 (pt0) cc_final: 0.8425 (pt0) REVERT: E 248 LEU cc_start: 0.8922 (tp) cc_final: 0.8580 (tp) REVERT: E 300 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7603 (mmtt) REVERT: E 323 LEU cc_start: 0.7989 (mt) cc_final: 0.7682 (mt) REVERT: D 37 PHE cc_start: 0.8294 (t80) cc_final: 0.7892 (t80) REVERT: D 53 ARG cc_start: 0.8614 (ttp80) cc_final: 0.8387 (ptm160) REVERT: D 66 ASN cc_start: 0.8211 (m-40) cc_final: 0.7963 (m-40) REVERT: D 81 ASP cc_start: 0.6909 (p0) cc_final: 0.6685 (p0) REVERT: D 141 LEU cc_start: 0.8730 (tp) cc_final: 0.8463 (tt) REVERT: D 143 ARG cc_start: 0.8330 (ttp-110) cc_final: 0.8026 (ttm-80) REVERT: D 147 ASN cc_start: 0.8427 (p0) cc_final: 0.8184 (p0) REVERT: D 179 GLN cc_start: 0.8645 (pt0) cc_final: 0.8416 (pt0) REVERT: D 196 GLU cc_start: 0.8090 (tp30) cc_final: 0.7805 (tp30) REVERT: D 246 TYR cc_start: 0.8315 (t80) cc_final: 0.7904 (t80) REVERT: D 277 VAL cc_start: 0.8821 (t) cc_final: 0.8503 (p) REVERT: D 285 LEU cc_start: 0.8815 (tp) cc_final: 0.8485 (tt) REVERT: D 288 THR cc_start: 0.8548 (m) cc_final: 0.8194 (p) REVERT: D 316 LEU cc_start: 0.8541 (mt) cc_final: 0.8255 (mt) REVERT: D 323 LEU cc_start: 0.8083 (mt) cc_final: 0.7774 (pp) REVERT: D 402 LEU cc_start: 0.8779 (mt) cc_final: 0.8569 (pp) outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 0.2928 time to fit residues: 223.5547 Evaluate side-chains 420 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS B 290 GLN C 133 HIS C 174 GLN E 290 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14545 Z= 0.254 Angle : 0.684 13.609 19745 Z= 0.358 Chirality : 0.048 0.230 2240 Planarity : 0.005 0.046 2435 Dihedral : 4.993 37.944 2220 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.43 % Allowed : 12.49 % Favored : 84.08 % 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: 0.72 (0.21), residues: 1700 helix: 2.37 (0.22), residues: 575 sheet: 0.81 (0.27), residues: 420 loop : -1.42 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 263 HIS 0.002 0.001 HIS D 133 PHE 0.021 0.002 PHE C 192 TYR 0.021 0.002 TYR D 325 ARG 0.008 0.001 ARG D 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 455 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8233 (t80) cc_final: 0.7963 (t80) REVERT: A 77 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7941 (pt0) REVERT: A 110 ASP cc_start: 0.8570 (t0) cc_final: 0.8368 (t0) REVERT: A 121 ASP cc_start: 0.8621 (p0) cc_final: 0.8319 (p0) REVERT: A 141 LEU cc_start: 0.8649 (tp) cc_final: 0.8357 (tt) REVERT: A 181 GLU cc_start: 0.7685 (tt0) cc_final: 0.7400 (tt0) REVERT: A 193 GLU cc_start: 0.8738 (pm20) cc_final: 0.8071 (pm20) REVERT: A 235 GLU cc_start: 0.7301 (tt0) cc_final: 0.7042 (tt0) REVERT: A 249 ILE cc_start: 0.8733 (tt) cc_final: 0.8495 (tp) REVERT: B 38 LEU cc_start: 0.8873 (mt) cc_final: 0.8404 (mt) REVERT: B 42 MET cc_start: 0.7760 (mpp) cc_final: 0.6786 (mpp) REVERT: B 49 ASP cc_start: 0.7968 (t0) cc_final: 0.7744 (t0) REVERT: B 121 ASP cc_start: 0.8540 (p0) cc_final: 0.8229 (p0) REVERT: B 243 GLN cc_start: 0.8606 (mt0) cc_final: 0.8403 (mt0) REVERT: B 287 MET cc_start: 0.8299 (ttm) cc_final: 0.7941 (ttm) REVERT: B 300 LYS cc_start: 0.7824 (mmtm) cc_final: 0.7469 (mptt) REVERT: B 408 LYS cc_start: 0.7932 (mmmm) cc_final: 0.7668 (mmtm) REVERT: B 409 ARG cc_start: 0.8381 (tpp80) cc_final: 0.8049 (tpt90) REVERT: C 311 MET cc_start: 0.8609 (mmt) cc_final: 0.8399 (mmm) REVERT: E 38 LEU cc_start: 0.8823 (mt) cc_final: 0.8490 (mt) REVERT: E 42 MET cc_start: 0.7844 (mpp) cc_final: 0.7204 (mpp) REVERT: E 121 ASP cc_start: 0.8503 (p0) cc_final: 0.8135 (p0) REVERT: E 171 MET cc_start: 0.7428 (mpp) cc_final: 0.6856 (mtm) REVERT: E 248 LEU cc_start: 0.8939 (tp) cc_final: 0.8609 (tp) REVERT: E 409 ARG cc_start: 0.8187 (tpp80) cc_final: 0.7872 (tpt90) REVERT: E 434 LYS cc_start: 0.5887 (OUTLIER) cc_final: 0.5655 (ttpp) REVERT: D 81 ASP cc_start: 0.6942 (p0) cc_final: 0.6727 (p0) REVERT: D 91 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8328 (mt0) REVERT: D 141 LEU cc_start: 0.8694 (tp) cc_final: 0.8474 (tt) REVERT: D 147 ASN cc_start: 0.8445 (p0) cc_final: 0.8218 (p0) REVERT: D 218 ASP cc_start: 0.8777 (p0) cc_final: 0.8571 (p0) REVERT: D 246 TYR cc_start: 0.8487 (t80) cc_final: 0.8171 (t80) REVERT: D 285 LEU cc_start: 0.8832 (tp) cc_final: 0.8548 (tt) REVERT: D 288 THR cc_start: 0.8775 (m) cc_final: 0.8357 (p) REVERT: D 298 LEU cc_start: 0.7945 (mt) cc_final: 0.7745 (mt) REVERT: D 300 LYS cc_start: 0.8288 (mptt) cc_final: 0.7871 (mptt) REVERT: D 324 GLU cc_start: 0.7070 (mt-10) cc_final: 0.6615 (mt-10) outliers start: 53 outliers final: 37 residues processed: 475 average time/residue: 0.2750 time to fit residues: 188.7771 Evaluate side-chains 440 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 400 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 292 SER Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 308 ASP Chi-restraints excluded: chain D residue 406 ARG Chi-restraints excluded: chain D residue 408 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 174 GLN E 133 HIS E 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14545 Z= 0.239 Angle : 0.619 12.481 19745 Z= 0.319 Chirality : 0.046 0.209 2240 Planarity : 0.004 0.041 2435 Dihedral : 4.659 36.866 2220 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.27 % Allowed : 14.37 % Favored : 81.36 % 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: 0.79 (0.21), residues: 1700 helix: 2.41 (0.22), residues: 575 sheet: 0.84 (0.27), residues: 420 loop : -1.36 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 263 HIS 0.002 0.001 HIS D 133 PHE 0.019 0.002 PHE A 192 TYR 0.021 0.002 TYR C 246 ARG 0.007 0.001 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 424 time to evaluate : 1.802 Fit side-chains REVERT: A 121 ASP cc_start: 0.8634 (p0) cc_final: 0.8269 (p0) REVERT: A 141 LEU cc_start: 0.8604 (tp) cc_final: 0.8383 (tt) REVERT: A 193 GLU cc_start: 0.8764 (pm20) cc_final: 0.8094 (pm20) REVERT: A 268 ILE cc_start: 0.7961 (mm) cc_final: 0.7616 (mt) REVERT: A 409 ARG cc_start: 0.7923 (tpp80) cc_final: 0.7334 (tpt90) REVERT: B 38 LEU cc_start: 0.8891 (mt) cc_final: 0.8421 (mt) REVERT: B 42 MET cc_start: 0.7681 (mpp) cc_final: 0.6680 (mpp) REVERT: B 49 ASP cc_start: 0.8048 (t0) cc_final: 0.7847 (t0) REVERT: B 121 ASP cc_start: 0.8550 (p0) cc_final: 0.8212 (p0) REVERT: B 243 GLN cc_start: 0.8642 (mt0) cc_final: 0.8412 (mt0) REVERT: B 300 LYS cc_start: 0.7927 (mmtm) cc_final: 0.7592 (mptt) REVERT: B 409 ARG cc_start: 0.8263 (tpp80) cc_final: 0.7789 (tpt90) REVERT: C 80 MET cc_start: 0.8344 (mmm) cc_final: 0.8087 (mmm) REVERT: C 235 GLU cc_start: 0.7361 (tt0) cc_final: 0.7080 (tt0) REVERT: C 300 LYS cc_start: 0.8217 (mptt) cc_final: 0.7727 (mptt) REVERT: E 105 ASP cc_start: 0.7215 (p0) cc_final: 0.6969 (p0) REVERT: E 121 ASP cc_start: 0.8514 (p0) cc_final: 0.8137 (p0) REVERT: E 181 GLU cc_start: 0.7650 (tt0) cc_final: 0.7364 (tt0) REVERT: E 248 LEU cc_start: 0.8962 (tp) cc_final: 0.8630 (tp) REVERT: E 270 MET cc_start: 0.7936 (pmm) cc_final: 0.7233 (pmm) REVERT: E 323 LEU cc_start: 0.8154 (mp) cc_final: 0.7912 (mt) REVERT: E 409 ARG cc_start: 0.8114 (tpp80) cc_final: 0.7854 (tpt90) REVERT: D 81 ASP cc_start: 0.6958 (p0) cc_final: 0.6738 (p0) REVERT: D 141 LEU cc_start: 0.8696 (tp) cc_final: 0.8396 (tt) REVERT: D 143 ARG cc_start: 0.8379 (ttp-110) cc_final: 0.8125 (ttm-80) REVERT: D 147 ASN cc_start: 0.8488 (p0) cc_final: 0.8242 (p0) REVERT: D 246 TYR cc_start: 0.8481 (t80) cc_final: 0.8216 (t80) REVERT: D 252 TYR cc_start: 0.8684 (m-80) cc_final: 0.8403 (m-80) REVERT: D 285 LEU cc_start: 0.8902 (tp) cc_final: 0.8524 (tp) REVERT: D 288 THR cc_start: 0.8831 (m) cc_final: 0.8397 (p) REVERT: D 300 LYS cc_start: 0.8240 (mptt) cc_final: 0.7942 (mptt) REVERT: D 426 ASN cc_start: 0.8317 (m-40) cc_final: 0.8100 (m-40) outliers start: 66 outliers final: 45 residues processed: 449 average time/residue: 0.2565 time to fit residues: 170.2710 Evaluate side-chains 435 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 390 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 427 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 103 optimal weight: 0.0870 chunk 155 optimal weight: 0.0270 chunk 164 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 GLN C 91 GLN C 174 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN E 290 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14545 Z= 0.180 Angle : 0.603 11.239 19745 Z= 0.309 Chirality : 0.044 0.204 2240 Planarity : 0.004 0.039 2435 Dihedral : 4.472 35.687 2220 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.37 % Allowed : 18.12 % Favored : 78.51 % 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: 0.83 (0.21), residues: 1700 helix: 2.48 (0.22), residues: 575 sheet: 0.96 (0.28), residues: 395 loop : -1.36 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 263 HIS 0.002 0.000 HIS B 133 PHE 0.019 0.002 PHE B 330 TYR 0.022 0.002 TYR C 246 ARG 0.007 0.001 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 408 time to evaluate : 1.582 Fit side-chains REVERT: A 121 ASP cc_start: 0.8613 (p0) cc_final: 0.8227 (p0) REVERT: A 193 GLU cc_start: 0.8779 (pm20) cc_final: 0.8120 (pm20) REVERT: A 249 ILE cc_start: 0.8741 (tp) cc_final: 0.8421 (tp) REVERT: A 258 ILE cc_start: 0.8671 (mm) cc_final: 0.8352 (tt) REVERT: A 268 ILE cc_start: 0.8008 (mm) cc_final: 0.7697 (mt) REVERT: A 409 ARG cc_start: 0.7884 (tpp80) cc_final: 0.7259 (tpt90) REVERT: A 426 ASN cc_start: 0.8316 (m-40) cc_final: 0.8100 (m110) REVERT: B 38 LEU cc_start: 0.8897 (mt) cc_final: 0.8464 (mt) REVERT: B 42 MET cc_start: 0.7596 (mpp) cc_final: 0.6686 (mpp) REVERT: B 121 ASP cc_start: 0.8511 (p0) cc_final: 0.8149 (p0) REVERT: B 243 GLN cc_start: 0.8661 (mt0) cc_final: 0.8441 (mt0) REVERT: B 251 MET cc_start: 0.8478 (ptp) cc_final: 0.8256 (ptp) REVERT: B 300 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7588 (mptt) REVERT: B 409 ARG cc_start: 0.8187 (tpp80) cc_final: 0.7745 (tpt90) REVERT: C 80 MET cc_start: 0.8386 (mmm) cc_final: 0.8110 (mmm) REVERT: C 251 MET cc_start: 0.8299 (ptp) cc_final: 0.7953 (ptt) REVERT: C 263 TRP cc_start: 0.7985 (m-10) cc_final: 0.7681 (m-10) REVERT: C 300 LYS cc_start: 0.8232 (mptt) cc_final: 0.7644 (mptt) REVERT: E 121 ASP cc_start: 0.8496 (p0) cc_final: 0.8088 (p0) REVERT: E 127 GLU cc_start: 0.7610 (tt0) cc_final: 0.7358 (tt0) REVERT: E 181 GLU cc_start: 0.7682 (tt0) cc_final: 0.7346 (tt0) REVERT: E 248 LEU cc_start: 0.8958 (tp) cc_final: 0.8654 (tp) REVERT: E 251 MET cc_start: 0.8382 (ptp) cc_final: 0.8089 (ptt) REVERT: E 324 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6668 (mt-10) REVERT: E 409 ARG cc_start: 0.7989 (tpp80) cc_final: 0.7718 (tpt90) REVERT: D 81 ASP cc_start: 0.6923 (p0) cc_final: 0.6687 (p0) REVERT: D 147 ASN cc_start: 0.8506 (p0) cc_final: 0.8245 (p0) REVERT: D 237 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7926 (ptp-170) REVERT: D 246 TYR cc_start: 0.8501 (t80) cc_final: 0.8260 (t80) REVERT: D 288 THR cc_start: 0.8852 (m) cc_final: 0.8386 (p) REVERT: D 300 LYS cc_start: 0.8215 (mptt) cc_final: 0.7889 (mptt) outliers start: 52 outliers final: 37 residues processed: 427 average time/residue: 0.2527 time to fit residues: 158.2587 Evaluate side-chains 434 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 396 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 413 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 2 optimal weight: 0.2980 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 147 optimal weight: 0.1980 chunk 41 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN C 174 GLN C 290 GLN E 290 GLN E 426 ASN D 426 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14545 Z= 0.192 Angle : 0.604 11.184 19745 Z= 0.306 Chirality : 0.044 0.203 2240 Planarity : 0.004 0.039 2435 Dihedral : 4.363 34.202 2220 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.21 % Allowed : 18.32 % Favored : 77.48 % 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: 0.79 (0.21), residues: 1700 helix: 2.34 (0.22), residues: 580 sheet: 0.98 (0.29), residues: 395 loop : -1.34 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 263 HIS 0.001 0.000 HIS B 133 PHE 0.018 0.001 PHE B 330 TYR 0.020 0.002 TYR B 246 ARG 0.006 0.000 ARG D 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 414 time to evaluate : 1.627 Fit side-chains REVERT: A 121 ASP cc_start: 0.8615 (p0) cc_final: 0.8204 (p0) REVERT: A 193 GLU cc_start: 0.8783 (pm20) cc_final: 0.8146 (pm20) REVERT: A 237 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7773 (ptp90) REVERT: A 249 ILE cc_start: 0.8732 (tp) cc_final: 0.8443 (tp) REVERT: A 250 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.7259 (mm-40) REVERT: A 258 ILE cc_start: 0.8694 (mm) cc_final: 0.8328 (tt) REVERT: A 268 ILE cc_start: 0.8024 (mm) cc_final: 0.7721 (mt) REVERT: A 409 ARG cc_start: 0.7867 (tpp80) cc_final: 0.7337 (tpt90) REVERT: A 426 ASN cc_start: 0.8351 (m-40) cc_final: 0.8143 (m110) REVERT: B 38 LEU cc_start: 0.8889 (mt) cc_final: 0.8455 (mt) REVERT: B 42 MET cc_start: 0.7595 (mpp) cc_final: 0.6727 (mpp) REVERT: B 89 ARG cc_start: 0.8255 (ttt-90) cc_final: 0.7595 (ttt-90) REVERT: B 121 ASP cc_start: 0.8511 (p0) cc_final: 0.8133 (p0) REVERT: B 243 GLN cc_start: 0.8657 (mt0) cc_final: 0.8431 (mt0) REVERT: B 300 LYS cc_start: 0.7953 (mmtm) cc_final: 0.7592 (mptt) REVERT: B 409 ARG cc_start: 0.8171 (tpp80) cc_final: 0.7733 (tpt90) REVERT: C 37 PHE cc_start: 0.8137 (t80) cc_final: 0.7829 (t80) REVERT: C 80 MET cc_start: 0.8426 (mmm) cc_final: 0.8147 (mmm) REVERT: C 268 ILE cc_start: 0.7771 (mm) cc_final: 0.7521 (mt) REVERT: C 300 LYS cc_start: 0.8255 (mptt) cc_final: 0.7716 (mptt) REVERT: E 105 ASP cc_start: 0.7210 (p0) cc_final: 0.6968 (p0) REVERT: E 121 ASP cc_start: 0.8511 (p0) cc_final: 0.8082 (p0) REVERT: E 127 GLU cc_start: 0.7678 (tt0) cc_final: 0.7425 (tt0) REVERT: E 181 GLU cc_start: 0.7703 (tt0) cc_final: 0.7332 (tt0) REVERT: E 248 LEU cc_start: 0.8988 (tp) cc_final: 0.8695 (tp) REVERT: E 330 PHE cc_start: 0.8280 (t80) cc_final: 0.8048 (t80) REVERT: E 409 ARG cc_start: 0.8028 (tpp80) cc_final: 0.7750 (tpt90) REVERT: D 147 ASN cc_start: 0.8523 (p0) cc_final: 0.8248 (p0) REVERT: D 246 TYR cc_start: 0.8529 (t80) cc_final: 0.8291 (t80) REVERT: D 300 LYS cc_start: 0.8205 (mptt) cc_final: 0.7844 (mptt) outliers start: 65 outliers final: 54 residues processed: 438 average time/residue: 0.2471 time to fit residues: 159.5326 Evaluate side-chains 443 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 387 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 413 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 86 optimal weight: 0.0470 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 174 GLN C 179 GLN C 290 GLN E 290 GLN D 55 ASN D 426 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14545 Z= 0.184 Angle : 0.611 10.808 19745 Z= 0.309 Chirality : 0.044 0.199 2240 Planarity : 0.004 0.038 2435 Dihedral : 4.284 32.748 2220 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.05 % Allowed : 18.25 % Favored : 76.70 % 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: 0.70 (0.21), residues: 1700 helix: 2.30 (0.22), residues: 580 sheet: 0.90 (0.28), residues: 405 loop : -1.43 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 263 HIS 0.001 0.000 HIS B 133 PHE 0.020 0.001 PHE C 319 TYR 0.021 0.002 TYR B 246 ARG 0.006 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 395 time to evaluate : 1.667 Fit side-chains REVERT: A 121 ASP cc_start: 0.8596 (p0) cc_final: 0.8176 (p0) REVERT: A 193 GLU cc_start: 0.8786 (pm20) cc_final: 0.8119 (pm20) REVERT: A 249 ILE cc_start: 0.8789 (tp) cc_final: 0.8450 (tp) REVERT: A 409 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7328 (tpt90) REVERT: B 38 LEU cc_start: 0.8888 (mt) cc_final: 0.8478 (mt) REVERT: B 42 MET cc_start: 0.7576 (mpp) cc_final: 0.6740 (mpp) REVERT: B 121 ASP cc_start: 0.8508 (p0) cc_final: 0.8122 (p0) REVERT: B 243 GLN cc_start: 0.8679 (mt0) cc_final: 0.8455 (mt0) REVERT: B 300 LYS cc_start: 0.7960 (mmtm) cc_final: 0.7555 (mptt) REVERT: B 409 ARG cc_start: 0.8153 (tpp80) cc_final: 0.7699 (tpt90) REVERT: C 37 PHE cc_start: 0.8204 (t80) cc_final: 0.7980 (t80) REVERT: C 80 MET cc_start: 0.8425 (mmm) cc_final: 0.8146 (mmm) REVERT: C 237 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8130 (ptp90) REVERT: C 251 MET cc_start: 0.8419 (ptp) cc_final: 0.7983 (ptt) REVERT: C 268 ILE cc_start: 0.7803 (mm) cc_final: 0.7524 (mt) REVERT: C 300 LYS cc_start: 0.8243 (mptt) cc_final: 0.7659 (mptt) REVERT: E 121 ASP cc_start: 0.8508 (p0) cc_final: 0.8068 (p0) REVERT: E 127 GLU cc_start: 0.7701 (tt0) cc_final: 0.7395 (tt0) REVERT: E 181 GLU cc_start: 0.7697 (tt0) cc_final: 0.7345 (tt0) REVERT: E 248 LEU cc_start: 0.8978 (tp) cc_final: 0.8696 (tp) REVERT: E 323 LEU cc_start: 0.8133 (mp) cc_final: 0.7912 (mt) REVERT: E 324 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6982 (mt-10) REVERT: E 409 ARG cc_start: 0.8022 (tpp80) cc_final: 0.7745 (tpt90) REVERT: D 147 ASN cc_start: 0.8532 (p0) cc_final: 0.8239 (p0) REVERT: D 288 THR cc_start: 0.8869 (m) cc_final: 0.8435 (p) REVERT: D 300 LYS cc_start: 0.8160 (mptt) cc_final: 0.7653 (mmtt) REVERT: D 316 LEU cc_start: 0.8399 (mm) cc_final: 0.8187 (mp) outliers start: 78 outliers final: 61 residues processed: 430 average time/residue: 0.2397 time to fit residues: 150.8395 Evaluate side-chains 465 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 403 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 308 ASP Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 428 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 138 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 ASN ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 GLN C 290 GLN E 290 GLN D 426 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14545 Z= 0.272 Angle : 0.642 10.944 19745 Z= 0.328 Chirality : 0.046 0.232 2240 Planarity : 0.004 0.039 2435 Dihedral : 4.360 32.717 2220 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.47 % Allowed : 20.26 % Favored : 75.28 % 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: 0.72 (0.21), residues: 1700 helix: 2.26 (0.22), residues: 585 sheet: 0.79 (0.27), residues: 425 loop : -1.36 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 263 HIS 0.003 0.001 HIS E 133 PHE 0.030 0.002 PHE D 37 TYR 0.022 0.002 TYR B 246 ARG 0.011 0.001 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 412 time to evaluate : 1.716 Fit side-chains REVERT: A 121 ASP cc_start: 0.8629 (p0) cc_final: 0.8204 (p0) REVERT: A 210 GLN cc_start: 0.8577 (mt0) cc_final: 0.8370 (mt0) REVERT: A 303 TYR cc_start: 0.7782 (p90) cc_final: 0.7450 (p90) REVERT: A 409 ARG cc_start: 0.7915 (tpp80) cc_final: 0.7458 (tpt90) REVERT: B 38 LEU cc_start: 0.8918 (mt) cc_final: 0.8473 (mt) REVERT: B 42 MET cc_start: 0.7633 (mpp) cc_final: 0.6745 (mpp) REVERT: B 121 ASP cc_start: 0.8580 (p0) cc_final: 0.8178 (p0) REVERT: B 243 GLN cc_start: 0.8674 (mt0) cc_final: 0.8451 (mt0) REVERT: B 300 LYS cc_start: 0.7992 (mmtm) cc_final: 0.7607 (mptt) REVERT: B 409 ARG cc_start: 0.8196 (tpp80) cc_final: 0.7767 (tpt90) REVERT: C 37 PHE cc_start: 0.8341 (t80) cc_final: 0.8097 (t80) REVERT: C 80 MET cc_start: 0.8502 (mmm) cc_final: 0.8212 (mmm) REVERT: C 237 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8146 (ptp90) REVERT: C 251 MET cc_start: 0.8620 (ptp) cc_final: 0.8262 (ptt) REVERT: C 300 LYS cc_start: 0.8279 (mptt) cc_final: 0.7698 (mptt) REVERT: C 316 LEU cc_start: 0.8499 (mt) cc_final: 0.8259 (mm) REVERT: E 80 MET cc_start: 0.8361 (mmt) cc_final: 0.7855 (mmt) REVERT: E 121 ASP cc_start: 0.8568 (p0) cc_final: 0.8127 (p0) REVERT: E 127 GLU cc_start: 0.7768 (tt0) cc_final: 0.7467 (tt0) REVERT: E 181 GLU cc_start: 0.7708 (tt0) cc_final: 0.7365 (tt0) REVERT: E 244 MET cc_start: 0.7848 (mtp) cc_final: 0.7645 (mtt) REVERT: E 248 LEU cc_start: 0.9029 (tp) cc_final: 0.8794 (tp) REVERT: E 323 LEU cc_start: 0.8173 (mp) cc_final: 0.7929 (mt) REVERT: E 324 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7026 (mt-10) REVERT: E 409 ARG cc_start: 0.8020 (tpp80) cc_final: 0.7746 (tpt90) REVERT: D 102 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.7139 (m-80) REVERT: D 147 ASN cc_start: 0.8537 (p0) cc_final: 0.8213 (p0) REVERT: D 285 LEU cc_start: 0.9146 (tt) cc_final: 0.8740 (tp) REVERT: D 288 THR cc_start: 0.8968 (m) cc_final: 0.8500 (p) REVERT: D 300 LYS cc_start: 0.8263 (mptt) cc_final: 0.7856 (mmtm) outliers start: 69 outliers final: 56 residues processed: 441 average time/residue: 0.2410 time to fit residues: 155.8421 Evaluate side-chains 461 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 403 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 427 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 104 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN B 290 GLN C 174 GLN C 290 GLN D 243 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14545 Z= 0.217 Angle : 0.630 10.586 19745 Z= 0.319 Chirality : 0.045 0.200 2240 Planarity : 0.004 0.038 2435 Dihedral : 4.317 30.485 2220 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.14 % Allowed : 21.49 % Favored : 74.37 % 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: 0.67 (0.21), residues: 1700 helix: 2.21 (0.22), residues: 585 sheet: 0.76 (0.27), residues: 425 loop : -1.39 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 263 HIS 0.002 0.001 HIS D 133 PHE 0.021 0.002 PHE D 37 TYR 0.021 0.002 TYR B 246 ARG 0.007 0.001 ARG D 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 413 time to evaluate : 1.719 Fit side-chains REVERT: A 121 ASP cc_start: 0.8608 (p0) cc_final: 0.8181 (p0) REVERT: A 409 ARG cc_start: 0.7877 (tpp80) cc_final: 0.7411 (tpt90) REVERT: B 38 LEU cc_start: 0.8903 (mt) cc_final: 0.8519 (mt) REVERT: B 42 MET cc_start: 0.7611 (mpp) cc_final: 0.6826 (mpp) REVERT: B 121 ASP cc_start: 0.8519 (p0) cc_final: 0.8103 (p0) REVERT: B 243 GLN cc_start: 0.8642 (mt0) cc_final: 0.8436 (mt0) REVERT: B 258 ILE cc_start: 0.8853 (mm) cc_final: 0.8416 (tt) REVERT: B 300 LYS cc_start: 0.7916 (mmtm) cc_final: 0.7583 (mptt) REVERT: B 409 ARG cc_start: 0.8166 (tpp80) cc_final: 0.7734 (tpt90) REVERT: C 37 PHE cc_start: 0.8334 (t80) cc_final: 0.8017 (t80) REVERT: C 80 MET cc_start: 0.8468 (mmm) cc_final: 0.8199 (mmm) REVERT: C 127 GLU cc_start: 0.7581 (tt0) cc_final: 0.7368 (tm-30) REVERT: C 237 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8149 (ptp90) REVERT: C 250 GLN cc_start: 0.7790 (mm110) cc_final: 0.7584 (mm110) REVERT: C 251 MET cc_start: 0.8632 (ptp) cc_final: 0.8147 (ptt) REVERT: C 300 LYS cc_start: 0.8282 (mptt) cc_final: 0.7663 (mptt) REVERT: E 121 ASP cc_start: 0.8560 (p0) cc_final: 0.8096 (p0) REVERT: E 127 GLU cc_start: 0.7746 (tt0) cc_final: 0.7452 (tt0) REVERT: E 181 GLU cc_start: 0.7685 (tt0) cc_final: 0.7343 (tt0) REVERT: E 248 LEU cc_start: 0.9041 (tp) cc_final: 0.8822 (tp) REVERT: E 323 LEU cc_start: 0.8210 (mp) cc_final: 0.7957 (mt) REVERT: E 324 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7034 (mt-10) REVERT: E 409 ARG cc_start: 0.8004 (tpp80) cc_final: 0.7682 (tpt90) REVERT: D 89 ARG cc_start: 0.8489 (ttt-90) cc_final: 0.7975 (ttt-90) REVERT: D 102 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.6991 (m-80) REVERT: D 147 ASN cc_start: 0.8537 (p0) cc_final: 0.8241 (p0) REVERT: D 285 LEU cc_start: 0.9092 (tt) cc_final: 0.8763 (tp) REVERT: D 288 THR cc_start: 0.9013 (m) cc_final: 0.8454 (p) REVERT: D 300 LYS cc_start: 0.8259 (mptt) cc_final: 0.7849 (mmtm) REVERT: D 316 LEU cc_start: 0.8397 (mm) cc_final: 0.8184 (mp) outliers start: 64 outliers final: 57 residues processed: 442 average time/residue: 0.2437 time to fit residues: 158.1550 Evaluate side-chains 463 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 404 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 428 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 66 optimal weight: 0.3980 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 144 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN A 334 GLN C 174 GLN D 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14545 Z= 0.218 Angle : 0.642 10.550 19745 Z= 0.323 Chirality : 0.045 0.199 2240 Planarity : 0.004 0.051 2435 Dihedral : 4.321 29.450 2220 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.88 % Allowed : 22.20 % Favored : 73.92 % 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: 0.62 (0.21), residues: 1700 helix: 2.17 (0.22), residues: 585 sheet: 0.74 (0.27), residues: 425 loop : -1.41 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 430 HIS 0.002 0.000 HIS E 133 PHE 0.020 0.002 PHE B 330 TYR 0.020 0.002 TYR B 246 ARG 0.011 0.001 ARG D 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 413 time to evaluate : 1.663 Fit side-chains revert: symmetry clash REVERT: A 121 ASP cc_start: 0.8606 (p0) cc_final: 0.8174 (p0) REVERT: A 409 ARG cc_start: 0.7880 (tpp80) cc_final: 0.7410 (tpt90) REVERT: B 38 LEU cc_start: 0.8904 (mt) cc_final: 0.8516 (mt) REVERT: B 42 MET cc_start: 0.7606 (mpp) cc_final: 0.6852 (mpp) REVERT: B 121 ASP cc_start: 0.8525 (p0) cc_final: 0.8102 (p0) REVERT: B 243 GLN cc_start: 0.8615 (mt0) cc_final: 0.8414 (mt0) REVERT: B 258 ILE cc_start: 0.8857 (mm) cc_final: 0.8414 (tt) REVERT: B 300 LYS cc_start: 0.7920 (mmtm) cc_final: 0.7576 (mptt) REVERT: B 409 ARG cc_start: 0.8174 (tpp80) cc_final: 0.7732 (tpt90) REVERT: C 37 PHE cc_start: 0.8357 (t80) cc_final: 0.8067 (t80) REVERT: C 80 MET cc_start: 0.8477 (mmm) cc_final: 0.8199 (mmm) REVERT: C 127 GLU cc_start: 0.7587 (tt0) cc_final: 0.7318 (tm-30) REVERT: C 237 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8116 (ptp90) REVERT: C 300 LYS cc_start: 0.8285 (mptt) cc_final: 0.7666 (mptt) REVERT: E 80 MET cc_start: 0.8379 (mmt) cc_final: 0.7880 (mmt) REVERT: E 121 ASP cc_start: 0.8567 (p0) cc_final: 0.8087 (p0) REVERT: E 127 GLU cc_start: 0.7742 (tt0) cc_final: 0.7447 (tt0) REVERT: E 181 GLU cc_start: 0.7678 (tt0) cc_final: 0.7349 (tt0) REVERT: E 248 LEU cc_start: 0.9060 (tp) cc_final: 0.8841 (tp) REVERT: E 323 LEU cc_start: 0.8211 (mp) cc_final: 0.7950 (mt) REVERT: E 324 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7076 (mt-10) REVERT: E 409 ARG cc_start: 0.8001 (tpp80) cc_final: 0.7680 (tpt90) REVERT: D 102 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.7024 (m-80) REVERT: D 147 ASN cc_start: 0.8555 (p0) cc_final: 0.8275 (p0) REVERT: D 300 LYS cc_start: 0.8309 (mptt) cc_final: 0.7892 (mmtm) outliers start: 60 outliers final: 53 residues processed: 441 average time/residue: 0.2389 time to fit residues: 155.3715 Evaluate side-chains 461 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 406 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 237 ARG Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 428 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 134 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 104 optimal weight: 0.0040 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 143 optimal weight: 0.4980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN B 334 GLN C 174 GLN C 334 GLN E 334 GLN D 91 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14545 Z= 0.198 Angle : 0.642 12.856 19745 Z= 0.321 Chirality : 0.045 0.334 2240 Planarity : 0.004 0.038 2435 Dihedral : 4.239 28.100 2220 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.50 % Allowed : 23.11 % Favored : 73.40 % 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: 0.53 (0.21), residues: 1700 helix: 2.11 (0.22), residues: 585 sheet: 0.80 (0.28), residues: 405 loop : -1.50 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 263 HIS 0.001 0.000 HIS E 133 PHE 0.025 0.001 PHE B 330 TYR 0.020 0.002 TYR B 246 ARG 0.008 0.001 ARG D 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 419 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 121 ASP cc_start: 0.8598 (p0) cc_final: 0.8158 (p0) REVERT: A 409 ARG cc_start: 0.7898 (tpp80) cc_final: 0.7442 (tpt90) REVERT: B 38 LEU cc_start: 0.8893 (mt) cc_final: 0.8500 (mt) REVERT: B 42 MET cc_start: 0.7600 (mpp) cc_final: 0.6830 (mpp) REVERT: B 121 ASP cc_start: 0.8521 (p0) cc_final: 0.8105 (p0) REVERT: B 127 GLU cc_start: 0.7837 (tp30) cc_final: 0.7561 (tp30) REVERT: B 189 ASP cc_start: 0.7957 (m-30) cc_final: 0.7738 (t0) REVERT: B 258 ILE cc_start: 0.8856 (mm) cc_final: 0.8410 (tt) REVERT: B 300 LYS cc_start: 0.7917 (mmtm) cc_final: 0.7664 (mptt) REVERT: B 324 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7155 (mm-30) REVERT: B 409 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7711 (tpt90) REVERT: C 42 MET cc_start: 0.7655 (mmm) cc_final: 0.7400 (ttt) REVERT: C 80 MET cc_start: 0.8451 (mmm) cc_final: 0.8187 (mmm) REVERT: C 127 GLU cc_start: 0.7576 (tt0) cc_final: 0.7251 (tm-30) REVERT: C 237 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.8096 (ptp90) REVERT: C 251 MET cc_start: 0.8667 (ptp) cc_final: 0.8422 (ptt) REVERT: C 300 LYS cc_start: 0.8268 (mptt) cc_final: 0.7641 (mptt) REVERT: E 80 MET cc_start: 0.8387 (mmt) cc_final: 0.7885 (mmt) REVERT: E 127 GLU cc_start: 0.7737 (tt0) cc_final: 0.7411 (tt0) REVERT: E 181 GLU cc_start: 0.7672 (tt0) cc_final: 0.7349 (tt0) REVERT: E 248 LEU cc_start: 0.9058 (tp) cc_final: 0.8844 (tp) REVERT: E 323 LEU cc_start: 0.8230 (mp) cc_final: 0.7764 (mt) REVERT: E 324 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7101 (mt-10) REVERT: E 409 ARG cc_start: 0.7993 (tpp80) cc_final: 0.7673 (tpt90) REVERT: D 89 ARG cc_start: 0.8484 (ttt-90) cc_final: 0.7863 (ttt-90) REVERT: D 91 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8209 (mt0) REVERT: D 102 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.7054 (m-80) REVERT: D 147 ASN cc_start: 0.8543 (p0) cc_final: 0.8263 (p0) REVERT: D 300 LYS cc_start: 0.8304 (mptt) cc_final: 0.7925 (mmtm) outliers start: 54 outliers final: 48 residues processed: 446 average time/residue: 0.2461 time to fit residues: 161.2166 Evaluate side-chains 458 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 407 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 294 SER Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 270 MET Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 413 VAL Chi-restraints excluded: chain D residue 428 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.0170 chunk 124 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 138 optimal weight: 0.3980 chunk 17 optimal weight: 0.0010 chunk 24 optimal weight: 0.7980 chunk 118 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 overall best weight: 0.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN B 334 GLN C 174 GLN C 334 GLN E 334 GLN D 91 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.096925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.086660 restraints weight = 27253.966| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.71 r_work: 0.3173 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 14545 Z= 0.245 Angle : 0.834 59.194 19745 Z= 0.464 Chirality : 0.048 0.691 2240 Planarity : 0.004 0.037 2435 Dihedral : 4.234 28.083 2220 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.56 % Allowed : 22.85 % Favored : 73.59 % Cbeta Deviations : 0.06 % 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: 0.51 (0.21), residues: 1700 helix: 2.09 (0.22), residues: 585 sheet: 0.77 (0.28), residues: 405 loop : -1.50 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 263 HIS 0.001 0.000 HIS E 133 PHE 0.022 0.001 PHE B 330 TYR 0.019 0.002 TYR B 246 ARG 0.007 0.001 ARG E 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3726.79 seconds wall clock time: 67 minutes 39.58 seconds (4059.58 seconds total)