Starting phenix.real_space_refine on Mon Aug 25 10:35:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bej_16005/08_2025/8bej_16005_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bej_16005/08_2025/8bej_16005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bej_16005/08_2025/8bej_16005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bej_16005/08_2025/8bej_16005.map" model { file = "/net/cci-nas-00/data/ceres_data/8bej_16005/08_2025/8bej_16005_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bej_16005/08_2025/8bej_16005_trim.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.007 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: 5 Type Number sf(0) Gaussians S 85 5.16 5 C 8835 2.51 5 N 2260 2.21 5 O 2470 1.98 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27065 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "B" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "C" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "D" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "E" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.31, per 1000 atoms: 0.20 Number of scatterers: 27065 At special positions: 0 Unit cell: (93.888, 91.28, 123.228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 O 2470 8.00 N 2260 7.00 C 8835 6.00 H 13415 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 205 " " NAG B 501 " - " ASN B 205 " " NAG C 501 " - " ASN C 205 " " NAG D 501 " - " ASN D 205 " " NAG E 501 " - " ASN E 205 " Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 42.3% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.572A pdb=" N THR A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 Processing helix chain 'A' and resid 90 through 97 removed outlier: 3.530A pdb=" N LEU A 93 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER A 95 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 97 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 233 through 246 Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 254 through 280 removed outlier: 3.518A pdb=" N PHE A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 314 Processing helix chain 'A' and resid 317 through 418 removed outlier: 4.017A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 15 through 27 removed outlier: 3.572A pdb=" N THR B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 79 Processing helix chain 'B' and resid 90 through 97 removed outlier: 3.531A pdb=" N LEU B 93 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER B 95 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 97 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 233 through 246 Processing helix chain 'B' and resid 247 through 250 Processing helix chain 'B' and resid 254 through 280 removed outlier: 3.518A pdb=" N PHE B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 314 Processing helix chain 'B' and resid 317 through 418 removed outlier: 4.016A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 15 through 27 removed outlier: 3.572A pdb=" N THR C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.530A pdb=" N LEU C 93 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER C 95 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 97 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 233 through 246 Processing helix chain 'C' and resid 247 through 250 Processing helix chain 'C' and resid 254 through 280 removed outlier: 3.519A pdb=" N PHE C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 314 Processing helix chain 'C' and resid 317 through 418 removed outlier: 4.016A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'D' and resid 15 through 27 removed outlier: 3.571A pdb=" N THR D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 79 Processing helix chain 'D' and resid 90 through 97 removed outlier: 3.530A pdb=" N LEU D 93 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER D 95 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 97 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 233 through 246 Processing helix chain 'D' and resid 247 through 250 Processing helix chain 'D' and resid 254 through 280 removed outlier: 3.518A pdb=" N PHE D 261 " --> pdb=" O ALA D 257 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU D 280 " --> pdb=" O ALA D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 314 Processing helix chain 'D' and resid 317 through 418 removed outlier: 4.016A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'E' and resid 15 through 27 removed outlier: 3.571A pdb=" N THR E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 79 Processing helix chain 'E' and resid 90 through 97 removed outlier: 3.530A pdb=" N LEU E 93 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER E 95 " --> pdb=" O LEU E 92 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE E 97 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 233 through 246 Processing helix chain 'E' and resid 247 through 250 Processing helix chain 'E' and resid 254 through 280 removed outlier: 3.518A pdb=" N PHE E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 314 Processing helix chain 'E' and resid 317 through 418 removed outlier: 4.016A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 4.415A pdb=" N LYS A 109 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 137 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU A 62 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL A 56 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR A 64 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE A 68 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL A 50 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA A 70 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N MET A 48 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR A 72 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N THR A 46 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N LYS A 74 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL A 44 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 124 removed outlier: 6.622A pdb=" N GLU A 62 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL A 56 " --> pdb=" O GLU A 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR A 64 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE A 68 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL A 50 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA A 70 " --> pdb=" O MET A 48 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N MET A 48 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR A 72 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N THR A 46 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N LYS A 74 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL A 44 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.498A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111 removed outlier: 4.414A pdb=" N LYS B 109 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 137 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU B 62 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL B 56 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B 64 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE B 68 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL B 50 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA B 70 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N MET B 48 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR B 72 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR B 46 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS B 74 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL B 44 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 124 removed outlier: 6.622A pdb=" N GLU B 62 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL B 56 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B 64 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE B 68 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL B 50 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA B 70 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N MET B 48 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR B 72 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR B 46 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS B 74 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL B 44 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.498A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111 removed outlier: 4.415A pdb=" N LYS C 109 " --> pdb=" O SER C 139 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 137 " --> pdb=" O PHE C 111 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU C 62 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL C 56 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR C 64 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE C 68 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL C 50 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA C 70 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N MET C 48 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR C 72 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR C 46 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS C 74 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL C 44 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 120 through 124 removed outlier: 6.623A pdb=" N GLU C 62 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL C 56 " --> pdb=" O GLU C 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR C 64 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE C 68 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL C 50 " --> pdb=" O PHE C 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA C 70 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N MET C 48 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR C 72 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR C 46 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS C 74 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N VAL C 44 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.499A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111 removed outlier: 4.415A pdb=" N LYS D 109 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 137 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU D 62 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL D 56 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR D 64 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE D 68 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL D 50 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA D 70 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N MET D 48 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR D 72 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR D 46 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS D 74 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL D 44 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 120 through 124 removed outlier: 6.622A pdb=" N GLU D 62 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N VAL D 56 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR D 64 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE D 68 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL D 50 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA D 70 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N MET D 48 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N THR D 72 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR D 46 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS D 74 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL D 44 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.498A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111 removed outlier: 4.414A pdb=" N LYS E 109 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR E 137 " --> pdb=" O PHE E 111 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU E 62 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL E 56 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR E 64 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE E 68 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL E 50 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA E 70 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N MET E 48 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR E 72 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR E 46 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS E 74 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL E 44 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 120 through 124 removed outlier: 6.621A pdb=" N GLU E 62 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL E 56 " --> pdb=" O GLU E 62 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR E 64 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE E 68 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL E 50 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA E 70 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N MET E 48 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N THR E 72 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N THR E 46 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS E 74 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N VAL E 44 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.498A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) 785 hydrogen bonds defined for protein. 2280 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: 7.48 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13415 1.03 - 1.23: 0 1.23 - 1.42: 6035 1.42 - 1.61: 7825 1.61 - 1.81: 150 Bond restraints: 27425 Sorted by residual: bond pdb=" N ASN C 14 " pdb=" H ASN C 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N ASN E 14 " pdb=" H ASN E 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N ASN A 14 " pdb=" H ASN A 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N ASN D 14 " pdb=" H ASN D 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" N ASN B 14 " pdb=" H ASN B 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.46e+01 ... (remaining 27420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 47967 1.14 - 2.28: 1259 2.28 - 3.42: 69 3.42 - 4.55: 35 4.55 - 5.69: 5 Bond angle restraints: 49335 Sorted by residual: angle pdb=" C MET A 115 " pdb=" N THR A 116 " pdb=" CA THR A 116 " ideal model delta sigma weight residual 121.70 127.39 -5.69 1.80e+00 3.09e-01 1.00e+01 angle pdb=" C MET D 115 " pdb=" N THR D 116 " pdb=" CA THR D 116 " ideal model delta sigma weight residual 121.70 127.39 -5.69 1.80e+00 3.09e-01 9.99e+00 angle pdb=" C MET C 115 " pdb=" N THR C 116 " pdb=" CA THR C 116 " ideal model delta sigma weight residual 121.70 127.33 -5.63 1.80e+00 3.09e-01 9.79e+00 angle pdb=" C MET E 115 " pdb=" N THR E 116 " pdb=" CA THR E 116 " ideal model delta sigma weight residual 121.70 127.33 -5.63 1.80e+00 3.09e-01 9.78e+00 angle pdb=" C MET B 115 " pdb=" N THR B 116 " pdb=" CA THR B 116 " ideal model delta sigma weight residual 121.70 127.33 -5.63 1.80e+00 3.09e-01 9.77e+00 ... (remaining 49330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.29: 12145 12.29 - 24.57: 690 24.57 - 36.86: 100 36.86 - 49.15: 80 49.15 - 61.44: 85 Dihedral angle restraints: 13100 sinusoidal: 6970 harmonic: 6130 Sorted by residual: dihedral pdb=" CB LYS A 315 " pdb=" CG LYS A 315 " pdb=" CD LYS A 315 " pdb=" CE LYS A 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.27 -40.27 3 1.50e+01 4.44e-03 7.17e+00 dihedral pdb=" CB LYS B 315 " pdb=" CG LYS B 315 " pdb=" CD LYS B 315 " pdb=" CE LYS B 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.26 -40.26 3 1.50e+01 4.44e-03 7.17e+00 dihedral pdb=" CB LYS E 315 " pdb=" CG LYS E 315 " pdb=" CD LYS E 315 " pdb=" CE LYS E 315 " ideal model delta sinusoidal sigma weight residual 60.00 100.25 -40.25 3 1.50e+01 4.44e-03 7.17e+00 ... (remaining 13097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1325 0.024 - 0.048: 519 0.048 - 0.071: 144 0.071 - 0.095: 78 0.095 - 0.119: 94 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ILE B 41 " pdb=" N ILE B 41 " pdb=" C ILE B 41 " pdb=" CB ILE B 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.55e-01 chirality pdb=" CA ILE E 41 " pdb=" N ILE E 41 " pdb=" C ILE E 41 " pdb=" CB ILE E 41 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 chirality pdb=" C1 NAG C 501 " pdb=" ND2 ASN C 205 " pdb=" C2 NAG C 501 " pdb=" O5 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 2157 not shown) Planarity restraints: 3980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 149 " 0.015 5.00e-02 4.00e+02 2.28e-02 8.35e-01 pdb=" N PRO B 150 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 150 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 150 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 149 " 0.015 5.00e-02 4.00e+02 2.28e-02 8.31e-01 pdb=" N PRO C 150 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO C 150 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 150 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 149 " -0.015 5.00e-02 4.00e+02 2.28e-02 8.29e-01 pdb=" N PRO E 150 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO E 150 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 150 " -0.012 5.00e-02 4.00e+02 ... (remaining 3977 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.29: 4682 2.29 - 2.87: 62535 2.87 - 3.45: 68581 3.45 - 4.02: 96053 4.02 - 4.60: 146626 Nonbonded interactions: 378477 Sorted by model distance: nonbonded pdb=" H ASN B 167 " pdb=" O GLU B 212 " model vdw 1.718 2.450 nonbonded pdb=" H ASN C 167 " pdb=" O GLU C 212 " model vdw 1.718 2.450 nonbonded pdb=" H ASN D 167 " pdb=" O GLU D 212 " model vdw 1.718 2.450 nonbonded pdb=" H ASN E 167 " pdb=" O GLU E 212 " model vdw 1.718 2.450 nonbonded pdb=" H ASN A 167 " pdb=" O GLU A 212 " model vdw 1.719 2.450 ... (remaining 378472 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.670 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: 0.160 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 30.730 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 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 : 0.002 0.017 14020 Z= 0.091 Angle : 0.375 5.693 19085 Z= 0.187 Chirality : 0.037 0.119 2160 Planarity : 0.003 0.023 2375 Dihedral : 6.958 61.435 5090 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.22), residues: 1670 helix: 2.94 (0.22), residues: 575 sheet: -0.22 (0.25), residues: 485 loop : 0.67 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 45 TYR 0.005 0.001 TYR B 285 PHE 0.003 0.001 PHE E 69 TRP 0.003 0.000 TRP B 73 HIS 0.002 0.001 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00196 (14010) covalent geometry : angle 0.37295 (19060) SS BOND : bond 0.00065 ( 5) SS BOND : angle 0.25153 ( 10) hydrogen bonds : bond 0.24481 ( 710) hydrogen bonds : angle 8.53769 ( 2280) link_NAG-ASN : bond 0.00090 ( 5) link_NAG-ASN : angle 1.35281 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 85 GLN cc_start: 0.8052 (mm110) cc_final: 0.7777 (mm110) REVERT: D 232 GLN cc_start: 0.9321 (tp40) cc_final: 0.9109 (tp40) REVERT: E 85 GLN cc_start: 0.8069 (mm110) cc_final: 0.7843 (mm110) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.3446 time to fit residues: 89.1774 Evaluate side-chains 124 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 199 GLN A 410 ASN B 85 GLN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN C 85 GLN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 ASN D 85 GLN D 199 GLN E 85 GLN E 199 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.064643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.054405 restraints weight = 128418.930| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.72 r_work: 0.2875 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 14020 Z= 0.299 Angle : 0.596 5.781 19085 Z= 0.322 Chirality : 0.043 0.152 2160 Planarity : 0.005 0.043 2375 Dihedral : 3.749 13.696 1955 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.20 % Allowed : 5.17 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.21), residues: 1670 helix: 2.41 (0.21), residues: 615 sheet: -0.03 (0.27), residues: 400 loop : 0.03 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 190 TYR 0.011 0.002 TYR B 297 PHE 0.021 0.002 PHE E 53 TRP 0.013 0.002 TRP A 174 HIS 0.002 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00654 (14010) covalent geometry : angle 0.59531 (19060) SS BOND : bond 0.00429 ( 5) SS BOND : angle 0.73558 ( 10) hydrogen bonds : bond 0.04762 ( 710) hydrogen bonds : angle 5.58292 ( 2280) link_NAG-ASN : bond 0.00125 ( 5) link_NAG-ASN : angle 1.18983 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.7492 (m100) cc_final: 0.7195 (m100) REVERT: A 216 MET cc_start: 0.8809 (mmm) cc_final: 0.8400 (mmm) REVERT: A 245 GLN cc_start: 0.8566 (mp10) cc_final: 0.8334 (tm-30) REVERT: B 61 MET cc_start: 0.8982 (mmm) cc_final: 0.8762 (tpp) REVERT: B 114 TRP cc_start: 0.7779 (m100) cc_final: 0.7412 (m100) REVERT: C 85 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8045 (mm110) REVERT: C 114 TRP cc_start: 0.7645 (m100) cc_final: 0.7286 (m100) REVERT: D 114 TRP cc_start: 0.7605 (m100) cc_final: 0.7216 (m100) REVERT: E 114 TRP cc_start: 0.7758 (m100) cc_final: 0.7400 (m100) outliers start: 3 outliers final: 3 residues processed: 141 average time/residue: 0.2845 time to fit residues: 59.5494 Evaluate side-chains 121 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 118 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain E residue 302 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 151 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 140 optimal weight: 0.2980 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN B 199 GLN B 410 ASN C 410 ASN E 410 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.066469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.056097 restraints weight = 129953.218| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 3.81 r_work: 0.2893 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14020 Z= 0.105 Angle : 0.437 4.662 19085 Z= 0.230 Chirality : 0.040 0.143 2160 Planarity : 0.004 0.043 2375 Dihedral : 3.348 11.694 1955 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.21), residues: 1670 helix: 3.09 (0.21), residues: 610 sheet: -0.22 (0.26), residues: 430 loop : 0.08 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.012 0.001 TYR B 297 PHE 0.010 0.001 PHE D 301 TRP 0.007 0.001 TRP C 73 HIS 0.003 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00216 (14010) covalent geometry : angle 0.43599 (19060) SS BOND : bond 0.00261 ( 5) SS BOND : angle 0.56144 ( 10) hydrogen bonds : bond 0.04126 ( 710) hydrogen bonds : angle 4.77424 ( 2280) link_NAG-ASN : bond 0.00189 ( 5) link_NAG-ASN : angle 1.03087 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.9279 (mmt) cc_final: 0.9037 (mmt) REVERT: A 85 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8128 (mm110) REVERT: A 114 TRP cc_start: 0.7435 (m100) cc_final: 0.7090 (m100) REVERT: A 245 GLN cc_start: 0.8571 (mp10) cc_final: 0.8302 (tm-30) REVERT: B 85 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8279 (mm-40) REVERT: B 114 TRP cc_start: 0.7687 (m100) cc_final: 0.7294 (m100) REVERT: B 216 MET cc_start: 0.8729 (mmm) cc_final: 0.8305 (mmm) REVERT: C 85 GLN cc_start: 0.8321 (mm-40) cc_final: 0.8073 (mm110) REVERT: C 114 TRP cc_start: 0.7609 (m100) cc_final: 0.7215 (m100) REVERT: D 114 TRP cc_start: 0.7515 (m100) cc_final: 0.7114 (m100) REVERT: D 245 GLN cc_start: 0.8591 (mp10) cc_final: 0.8290 (tm-30) REVERT: E 114 TRP cc_start: 0.7737 (m100) cc_final: 0.7358 (m100) REVERT: E 216 MET cc_start: 0.8714 (mmm) cc_final: 0.8172 (mmm) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.2965 time to fit residues: 56.6093 Evaluate side-chains 122 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 GLN E 410 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.064280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.054044 restraints weight = 132132.341| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.67 r_work: 0.2837 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 14020 Z= 0.256 Angle : 0.516 4.865 19085 Z= 0.279 Chirality : 0.041 0.139 2160 Planarity : 0.005 0.043 2375 Dihedral : 3.710 13.150 1955 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.27 % Allowed : 5.84 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.21), residues: 1670 helix: 2.89 (0.21), residues: 610 sheet: -0.46 (0.26), residues: 410 loop : -0.28 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 190 TYR 0.018 0.001 TYR B 297 PHE 0.010 0.002 PHE C 402 TRP 0.007 0.001 TRP C 414 HIS 0.003 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00559 (14010) covalent geometry : angle 0.51506 (19060) SS BOND : bond 0.00328 ( 5) SS BOND : angle 0.73819 ( 10) hydrogen bonds : bond 0.03988 ( 710) hydrogen bonds : angle 4.80327 ( 2280) link_NAG-ASN : bond 0.00029 ( 5) link_NAG-ASN : angle 1.21805 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8165 (mm110) REVERT: A 114 TRP cc_start: 0.7533 (m100) cc_final: 0.7155 (m100) REVERT: B 85 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8313 (mm110) REVERT: B 114 TRP cc_start: 0.7764 (m100) cc_final: 0.7329 (m100) REVERT: B 306 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8910 (tm-30) REVERT: C 114 TRP cc_start: 0.7685 (m100) cc_final: 0.7246 (m100) REVERT: C 306 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8905 (tm-30) REVERT: D 114 TRP cc_start: 0.7644 (m100) cc_final: 0.7190 (m100) REVERT: E 114 TRP cc_start: 0.7753 (m100) cc_final: 0.7333 (m100) REVERT: E 306 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8916 (tm-30) outliers start: 4 outliers final: 4 residues processed: 120 average time/residue: 0.2611 time to fit residues: 48.1685 Evaluate side-chains 119 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain C residue 199 GLN Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 94 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 121 optimal weight: 0.3980 chunk 98 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 46 optimal weight: 0.0670 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.066104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.055649 restraints weight = 131014.779| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.80 r_work: 0.2851 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14020 Z= 0.118 Angle : 0.432 4.418 19085 Z= 0.227 Chirality : 0.040 0.141 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.435 12.354 1955 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.13 % Allowed : 6.31 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.21), residues: 1670 helix: 3.23 (0.21), residues: 610 sheet: -0.16 (0.27), residues: 380 loop : -0.30 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.012 0.001 TYR B 297 PHE 0.028 0.001 PHE A 301 TRP 0.007 0.001 TRP C 73 HIS 0.002 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00248 (14010) covalent geometry : angle 0.43073 (19060) SS BOND : bond 0.00265 ( 5) SS BOND : angle 0.64728 ( 10) hydrogen bonds : bond 0.03581 ( 710) hydrogen bonds : angle 4.48157 ( 2280) link_NAG-ASN : bond 0.00129 ( 5) link_NAG-ASN : angle 1.03326 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.7576 (m100) cc_final: 0.7194 (m100) REVERT: A 216 MET cc_start: 0.8692 (mmm) cc_final: 0.8372 (mmm) REVERT: A 245 GLN cc_start: 0.7943 (tm-30) cc_final: 0.7691 (tm-30) REVERT: B 114 TRP cc_start: 0.7777 (m100) cc_final: 0.7335 (m100) REVERT: B 216 MET cc_start: 0.8777 (mmm) cc_final: 0.8230 (mmm) REVERT: C 85 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8172 (mm110) REVERT: C 114 TRP cc_start: 0.7624 (m100) cc_final: 0.7189 (m100) REVERT: D 114 TRP cc_start: 0.7622 (m100) cc_final: 0.7194 (m100) REVERT: D 216 MET cc_start: 0.8626 (mmm) cc_final: 0.7981 (mmm) REVERT: D 245 GLN cc_start: 0.8611 (mp10) cc_final: 0.8311 (tm-30) REVERT: E 114 TRP cc_start: 0.7771 (m100) cc_final: 0.7358 (m100) outliers start: 2 outliers final: 0 residues processed: 125 average time/residue: 0.2629 time to fit residues: 49.5389 Evaluate side-chains 119 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 106 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.064414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.054007 restraints weight = 133429.442| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.69 r_work: 0.2816 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 14020 Z= 0.303 Angle : 0.530 4.864 19085 Z= 0.289 Chirality : 0.042 0.153 2160 Planarity : 0.005 0.042 2375 Dihedral : 3.830 13.931 1955 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.34 % Allowed : 7.32 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.20), residues: 1670 helix: 2.93 (0.21), residues: 585 sheet: -0.80 (0.24), residues: 440 loop : -0.40 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.018 0.002 TYR B 297 PHE 0.011 0.002 PHE A 301 TRP 0.006 0.001 TRP C 73 HIS 0.003 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00657 (14010) covalent geometry : angle 0.52867 (19060) SS BOND : bond 0.00280 ( 5) SS BOND : angle 0.77561 ( 10) hydrogen bonds : bond 0.03905 ( 710) hydrogen bonds : angle 4.78677 ( 2280) link_NAG-ASN : bond 0.00069 ( 5) link_NAG-ASN : angle 1.22069 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8139 (mm110) REVERT: A 114 TRP cc_start: 0.7578 (m100) cc_final: 0.7193 (m100) REVERT: A 245 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7797 (tm-30) REVERT: B 85 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8287 (mm110) REVERT: B 114 TRP cc_start: 0.7814 (m100) cc_final: 0.7344 (m100) REVERT: B 306 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8946 (tm-30) REVERT: C 114 TRP cc_start: 0.7703 (m100) cc_final: 0.7292 (m100) REVERT: D 114 TRP cc_start: 0.7630 (m100) cc_final: 0.7174 (m100) REVERT: E 114 TRP cc_start: 0.7815 (m100) cc_final: 0.7377 (m100) outliers start: 5 outliers final: 4 residues processed: 115 average time/residue: 0.2425 time to fit residues: 42.5123 Evaluate side-chains 115 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain D residue 302 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 78 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.065422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.055087 restraints weight = 130951.604| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.80 r_work: 0.2832 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 14020 Z= 0.122 Angle : 0.435 4.998 19085 Z= 0.228 Chirality : 0.040 0.182 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.489 12.546 1955 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.07 % Allowed : 7.45 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.21), residues: 1670 helix: 3.29 (0.20), residues: 610 sheet: -0.33 (0.27), residues: 380 loop : -0.39 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.016 0.001 TYR B 297 PHE 0.016 0.001 PHE A 301 TRP 0.007 0.001 TRP C 73 HIS 0.002 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00257 (14010) covalent geometry : angle 0.43368 (19060) SS BOND : bond 0.00282 ( 5) SS BOND : angle 0.69855 ( 10) hydrogen bonds : bond 0.03456 ( 710) hydrogen bonds : angle 4.41441 ( 2280) link_NAG-ASN : bond 0.00127 ( 5) link_NAG-ASN : angle 1.03643 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.7579 (m100) cc_final: 0.7187 (m100) REVERT: A 216 MET cc_start: 0.8677 (mmm) cc_final: 0.8339 (mmm) REVERT: A 245 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7788 (tm-30) REVERT: B 60 GLU cc_start: 0.9200 (mp0) cc_final: 0.8752 (mp0) REVERT: B 114 TRP cc_start: 0.7826 (m100) cc_final: 0.7371 (m100) REVERT: B 216 MET cc_start: 0.8821 (mmm) cc_final: 0.8213 (mmm) REVERT: B 306 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8884 (tm-30) REVERT: C 114 TRP cc_start: 0.7698 (m100) cc_final: 0.7279 (m100) REVERT: C 232 GLN cc_start: 0.9371 (tp40) cc_final: 0.9161 (tp40) REVERT: D 114 TRP cc_start: 0.7629 (m100) cc_final: 0.7211 (m100) REVERT: D 216 MET cc_start: 0.8638 (mmm) cc_final: 0.8032 (mmm) REVERT: D 245 GLN cc_start: 0.8637 (mp10) cc_final: 0.8333 (tm-30) REVERT: E 114 TRP cc_start: 0.7792 (m100) cc_final: 0.7362 (m100) outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.2457 time to fit residues: 44.8819 Evaluate side-chains 120 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 133 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 chunk 121 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.066595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.056244 restraints weight = 131758.296| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.63 r_work: 0.2898 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14020 Z= 0.151 Angle : 0.445 4.766 19085 Z= 0.235 Chirality : 0.040 0.172 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.483 12.561 1955 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.27 % Allowed : 7.32 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.21), residues: 1670 helix: 3.31 (0.20), residues: 610 sheet: -0.33 (0.28), residues: 380 loop : -0.41 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.011 0.001 TYR E 297 PHE 0.013 0.001 PHE A 301 TRP 0.006 0.001 TRP C 73 HIS 0.002 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00324 (14010) covalent geometry : angle 0.44366 (19060) SS BOND : bond 0.00256 ( 5) SS BOND : angle 0.73476 ( 10) hydrogen bonds : bond 0.03418 ( 710) hydrogen bonds : angle 4.38178 ( 2280) link_NAG-ASN : bond 0.00066 ( 5) link_NAG-ASN : angle 1.04554 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 123 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.7527 (m100) cc_final: 0.7132 (m100) REVERT: A 216 MET cc_start: 0.8675 (mmm) cc_final: 0.8393 (mmm) REVERT: A 245 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7851 (tm-30) REVERT: B 60 GLU cc_start: 0.9159 (mp0) cc_final: 0.8693 (mp0) REVERT: B 85 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8284 (mm110) REVERT: B 114 TRP cc_start: 0.7766 (m100) cc_final: 0.7312 (m100) REVERT: B 306 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8882 (tm-30) REVERT: C 114 TRP cc_start: 0.7618 (m100) cc_final: 0.7182 (m100) REVERT: C 232 GLN cc_start: 0.9355 (tp40) cc_final: 0.9155 (tp40) REVERT: D 114 TRP cc_start: 0.7553 (m100) cc_final: 0.7127 (m100) REVERT: D 216 MET cc_start: 0.8605 (mmm) cc_final: 0.8023 (mmm) REVERT: D 245 GLN cc_start: 0.8648 (mp10) cc_final: 0.8350 (tm-30) REVERT: E 114 TRP cc_start: 0.7764 (m100) cc_final: 0.7328 (m100) outliers start: 4 outliers final: 2 residues processed: 125 average time/residue: 0.2400 time to fit residues: 45.0512 Evaluate side-chains 120 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 70 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.066188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.055873 restraints weight = 131515.344| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.64 r_work: 0.2891 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 14020 Z= 0.166 Angle : 0.449 4.766 19085 Z= 0.238 Chirality : 0.040 0.174 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.498 12.541 1955 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.13 % Allowed : 7.58 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.21), residues: 1670 helix: 3.29 (0.20), residues: 610 sheet: -0.34 (0.28), residues: 380 loop : -0.47 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.017 0.001 TYR B 297 PHE 0.013 0.001 PHE A 301 TRP 0.006 0.001 TRP E 73 HIS 0.002 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00358 (14010) covalent geometry : angle 0.44814 (19060) SS BOND : bond 0.00268 ( 5) SS BOND : angle 0.77260 ( 10) hydrogen bonds : bond 0.03397 ( 710) hydrogen bonds : angle 4.37926 ( 2280) link_NAG-ASN : bond 0.00053 ( 5) link_NAG-ASN : angle 1.05199 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.7558 (m100) cc_final: 0.7158 (m100) REVERT: A 239 MET cc_start: 0.8887 (mmm) cc_final: 0.8612 (mmt) REVERT: A 245 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7893 (tm-30) REVERT: B 60 GLU cc_start: 0.9164 (mp0) cc_final: 0.8704 (mp0) REVERT: B 85 GLN cc_start: 0.8523 (mm-40) cc_final: 0.8303 (mm110) REVERT: B 114 TRP cc_start: 0.7756 (m100) cc_final: 0.7316 (m100) REVERT: B 216 MET cc_start: 0.8803 (mmm) cc_final: 0.8265 (mmm) REVERT: B 306 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8898 (tm-30) REVERT: C 114 TRP cc_start: 0.7636 (m100) cc_final: 0.7200 (m100) REVERT: D 114 TRP cc_start: 0.7571 (m100) cc_final: 0.7132 (m100) REVERT: D 216 MET cc_start: 0.8619 (mmm) cc_final: 0.8011 (mmm) REVERT: D 245 GLN cc_start: 0.8654 (mp10) cc_final: 0.8329 (tm-30) REVERT: E 114 TRP cc_start: 0.7760 (m100) cc_final: 0.7329 (m100) outliers start: 2 outliers final: 1 residues processed: 123 average time/residue: 0.2183 time to fit residues: 40.2140 Evaluate side-chains 119 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 108 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 139 optimal weight: 0.0270 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.065045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.054996 restraints weight = 131904.908| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.75 r_work: 0.2847 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14020 Z= 0.114 Angle : 0.435 5.095 19085 Z= 0.227 Chirality : 0.040 0.175 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.397 12.435 1955 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.07 % Allowed : 7.85 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.21), residues: 1670 helix: 3.39 (0.20), residues: 615 sheet: -0.26 (0.28), residues: 380 loop : -0.39 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.015 0.001 TYR B 297 PHE 0.012 0.001 PHE A 301 TRP 0.006 0.001 TRP C 73 HIS 0.002 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00245 (14010) covalent geometry : angle 0.43383 (19060) SS BOND : bond 0.00244 ( 5) SS BOND : angle 0.73596 ( 10) hydrogen bonds : bond 0.03296 ( 710) hydrogen bonds : angle 4.26336 ( 2280) link_NAG-ASN : bond 0.00113 ( 5) link_NAG-ASN : angle 1.01902 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8409 (mm-40) cc_final: 0.8158 (mm110) REVERT: A 114 TRP cc_start: 0.7652 (m100) cc_final: 0.7252 (m100) REVERT: A 216 MET cc_start: 0.8644 (mmm) cc_final: 0.8345 (mmm) REVERT: A 245 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7864 (tm-30) REVERT: B 60 GLU cc_start: 0.9215 (mp0) cc_final: 0.8725 (mp0) REVERT: B 114 TRP cc_start: 0.7847 (m100) cc_final: 0.7415 (m100) REVERT: B 216 MET cc_start: 0.8791 (mmm) cc_final: 0.8181 (mmm) REVERT: B 245 GLN cc_start: 0.8760 (mp10) cc_final: 0.8306 (tm-30) REVERT: B 306 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8818 (tm-30) REVERT: C 114 TRP cc_start: 0.7694 (m100) cc_final: 0.7263 (m100) REVERT: C 216 MET cc_start: 0.8625 (mmm) cc_final: 0.8024 (mmm) REVERT: D 114 TRP cc_start: 0.7667 (m100) cc_final: 0.7233 (m100) REVERT: D 245 GLN cc_start: 0.8635 (mp10) cc_final: 0.8325 (tm-30) REVERT: E 114 TRP cc_start: 0.7778 (m100) cc_final: 0.7348 (m100) REVERT: E 245 GLN cc_start: 0.8794 (mp10) cc_final: 0.8351 (tm-30) outliers start: 1 outliers final: 1 residues processed: 123 average time/residue: 0.2703 time to fit residues: 50.2252 Evaluate side-chains 122 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.066273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.055928 restraints weight = 131112.728| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.63 r_work: 0.2873 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 14020 Z= 0.179 Angle : 0.459 5.149 19085 Z= 0.244 Chirality : 0.040 0.166 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.496 12.423 1955 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.07 % Allowed : 7.92 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.21), residues: 1670 helix: 3.29 (0.20), residues: 615 sheet: -0.34 (0.28), residues: 380 loop : -0.48 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.014 0.001 TYR B 297 PHE 0.011 0.001 PHE B 301 TRP 0.005 0.001 TRP C 73 HIS 0.002 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00386 (14010) covalent geometry : angle 0.45852 (19060) SS BOND : bond 0.00259 ( 5) SS BOND : angle 0.72809 ( 10) hydrogen bonds : bond 0.03397 ( 710) hydrogen bonds : angle 4.35790 ( 2280) link_NAG-ASN : bond 0.00041 ( 5) link_NAG-ASN : angle 1.06091 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4588.53 seconds wall clock time: 79 minutes 15.59 seconds (4755.59 seconds total)