Starting phenix.real_space_refine on Sun May 25 21:32:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bej_16005/05_2025/8bej_16005_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bej_16005/05_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_16005/05_2025/8bej_16005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bej_16005/05_2025/8bej_16005.map" model { file = "/net/cci-nas-00/data/ceres_data/8bej_16005/05_2025/8bej_16005_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bej_16005/05_2025/8bej_16005_trim.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 14.37, per 1000 atoms: 0.53 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: 7.26 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 2.32 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: 10.61 Time building geometry restraints manager: 8.59 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 8.810 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: 0.450 Extract box with map and model: 1.010 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 58.400 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.580 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (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 TRP 0.003 0.000 TRP B 73 HIS 0.002 0.001 HIS C 195 PHE 0.003 0.001 PHE E 69 TYR 0.005 0.001 TYR B 285 ARG 0.001 0.000 ARG C 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00090 ( 5) link_NAG-ASN : angle 1.35281 ( 15) hydrogen bonds : bond 0.24481 ( 710) hydrogen bonds : angle 8.53769 ( 2280) SS BOND : bond 0.00065 ( 5) SS BOND : angle 0.25153 ( 10) covalent geometry : bond 0.00196 (14010) covalent geometry : angle 0.37295 (19060) *********************** 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 : 1.932 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: 0.6845 time to fit residues: 176.2265 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 : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.064073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053836 restraints weight = 129575.919| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.71 r_work: 0.2848 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 14020 Z= 0.337 Angle : 0.622 5.838 19085 Z= 0.338 Chirality : 0.044 0.150 2160 Planarity : 0.005 0.043 2375 Dihedral : 3.852 14.335 1955 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.54 % Allowed : 5.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1670 helix: 2.35 (0.21), residues: 615 sheet: -0.20 (0.26), residues: 410 loop : -0.01 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 174 HIS 0.002 0.001 HIS E 105 PHE 0.020 0.002 PHE E 53 TYR 0.012 0.002 TYR B 297 ARG 0.005 0.001 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00059 ( 5) link_NAG-ASN : angle 1.24652 ( 15) hydrogen bonds : bond 0.04871 ( 710) hydrogen bonds : angle 5.64710 ( 2280) SS BOND : bond 0.00396 ( 5) SS BOND : angle 0.76876 ( 10) covalent geometry : bond 0.00731 (14010) covalent geometry : angle 0.62092 (19060) *********************** 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 145 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 2.177 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 114 TRP cc_start: 0.7535 (m100) cc_final: 0.7212 (m100) REVERT: B 61 MET cc_start: 0.8967 (mmm) cc_final: 0.8738 (tpp) REVERT: B 114 TRP cc_start: 0.7798 (m100) cc_final: 0.7448 (m100) REVERT: C 85 GLN cc_start: 0.8291 (mm-40) cc_final: 0.8019 (mm110) REVERT: C 114 TRP cc_start: 0.7665 (m100) cc_final: 0.7311 (m100) REVERT: D 114 TRP cc_start: 0.7645 (m100) cc_final: 0.7259 (m100) REVERT: E 114 TRP cc_start: 0.7781 (m100) cc_final: 0.7397 (m100) outliers start: 8 outliers final: 6 residues processed: 145 average time/residue: 0.5962 time to fit residues: 128.8895 Evaluate side-chains 121 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 302 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain D 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 49 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 151 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** B 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN C 199 GLN 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 = 0.3272 r_free = 0.3272 target = 0.066188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.055736 restraints weight = 130317.132| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.78 r_work: 0.2859 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14020 Z= 0.129 Angle : 0.451 4.654 19085 Z= 0.239 Chirality : 0.040 0.143 2160 Planarity : 0.004 0.043 2375 Dihedral : 3.455 11.682 1955 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.07 % Allowed : 6.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.21), residues: 1670 helix: 3.00 (0.21), residues: 610 sheet: 0.03 (0.27), residues: 380 loop : -0.13 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 414 HIS 0.002 0.001 HIS A 105 PHE 0.009 0.001 PHE D 301 TYR 0.014 0.001 TYR B 297 ARG 0.003 0.000 ARG C 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 5) link_NAG-ASN : angle 0.98944 ( 15) hydrogen bonds : bond 0.04264 ( 710) hydrogen bonds : angle 4.92453 ( 2280) SS BOND : bond 0.00250 ( 5) SS BOND : angle 0.55778 ( 10) covalent geometry : bond 0.00266 (14010) covalent geometry : angle 0.44982 (19060) *********************** 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 129 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 2.367 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 85 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8153 (mm110) REVERT: A 114 TRP cc_start: 0.7492 (m100) cc_final: 0.7149 (m100) REVERT: B 114 TRP cc_start: 0.7753 (m100) cc_final: 0.7324 (m100) REVERT: C 85 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8069 (mm110) REVERT: C 114 TRP cc_start: 0.7654 (m100) cc_final: 0.7245 (m100) REVERT: D 114 TRP cc_start: 0.7558 (m100) cc_final: 0.7156 (m100) REVERT: D 245 GLN cc_start: 0.8585 (mp10) cc_final: 0.8298 (tm-30) REVERT: E 114 TRP cc_start: 0.7763 (m100) cc_final: 0.7369 (m100) REVERT: E 216 MET cc_start: 0.8742 (mmm) cc_final: 0.8159 (mmm) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.5952 time to fit residues: 115.6734 Evaluate side-chains 118 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 32 optimal weight: 0.0870 chunk 129 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN C 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.066965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.056546 restraints weight = 130833.061| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.78 r_work: 0.2869 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14020 Z= 0.113 Angle : 0.434 4.392 19085 Z= 0.228 Chirality : 0.040 0.143 2160 Planarity : 0.004 0.043 2375 Dihedral : 3.344 12.161 1955 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.21), residues: 1670 helix: 3.17 (0.21), residues: 610 sheet: 0.04 (0.27), residues: 380 loop : -0.18 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 414 HIS 0.003 0.001 HIS B 195 PHE 0.010 0.001 PHE A 301 TYR 0.017 0.001 TYR B 297 ARG 0.007 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 5) link_NAG-ASN : angle 1.01566 ( 15) hydrogen bonds : bond 0.03631 ( 710) hydrogen bonds : angle 4.52082 ( 2280) SS BOND : bond 0.00262 ( 5) SS BOND : angle 0.62103 ( 10) covalent geometry : bond 0.00240 (14010) covalent geometry : angle 0.43302 (19060) *********************** 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 128 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 2.294 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: A 114 TRP cc_start: 0.7542 (m100) cc_final: 0.7200 (m100) REVERT: A 245 GLN cc_start: 0.8673 (mp10) cc_final: 0.8250 (tm-30) REVERT: B 114 TRP cc_start: 0.7732 (m100) cc_final: 0.7280 (m100) REVERT: B 216 MET cc_start: 0.8755 (mmm) cc_final: 0.8257 (mmm) REVERT: C 85 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8082 (mm110) REVERT: C 114 TRP cc_start: 0.7672 (m100) cc_final: 0.7252 (m100) REVERT: D 114 TRP cc_start: 0.7592 (m100) cc_final: 0.7164 (m100) REVERT: D 216 MET cc_start: 0.8621 (mmm) cc_final: 0.7985 (mmm) REVERT: D 245 GLN cc_start: 0.8619 (mp10) cc_final: 0.8323 (tm-30) REVERT: D 306 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8837 (tm-30) REVERT: E 114 TRP cc_start: 0.7744 (m100) cc_final: 0.7342 (m100) outliers start: 3 outliers final: 0 residues processed: 127 average time/residue: 0.5565 time to fit residues: 106.1003 Evaluate side-chains 120 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 21 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.065737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.055301 restraints weight = 130862.404| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.76 r_work: 0.2849 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 14020 Z= 0.157 Angle : 0.445 4.470 19085 Z= 0.235 Chirality : 0.040 0.164 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.415 12.622 1955 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.20 % Allowed : 5.97 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.21), residues: 1670 helix: 3.22 (0.20), residues: 610 sheet: -0.09 (0.27), residues: 380 loop : -0.27 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 414 HIS 0.002 0.001 HIS D 105 PHE 0.023 0.001 PHE A 301 TYR 0.016 0.001 TYR D 297 ARG 0.004 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 5) link_NAG-ASN : angle 1.05248 ( 15) hydrogen bonds : bond 0.03583 ( 710) hydrogen bonds : angle 4.47897 ( 2280) SS BOND : bond 0.00265 ( 5) SS BOND : angle 0.72620 ( 10) covalent geometry : bond 0.00337 (14010) covalent geometry : angle 0.44356 (19060) *********************** 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 122 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 119 time to evaluate : 2.185 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: 0.7614 (m100) cc_final: 0.7236 (m100) REVERT: A 245 GLN cc_start: 0.8721 (mp10) cc_final: 0.8289 (tm-30) REVERT: B 60 GLU cc_start: 0.9168 (mp0) cc_final: 0.8719 (mp0) REVERT: B 114 TRP cc_start: 0.7781 (m100) cc_final: 0.7320 (m100) REVERT: B 216 MET cc_start: 0.8758 (mmm) cc_final: 0.8231 (mmm) REVERT: B 306 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8908 (tm-30) REVERT: C 85 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8148 (mm110) REVERT: C 114 TRP cc_start: 0.7668 (m100) cc_final: 0.7243 (m100) REVERT: D 114 TRP cc_start: 0.7624 (m100) cc_final: 0.7184 (m100) REVERT: D 245 GLN cc_start: 0.8628 (mp10) cc_final: 0.8308 (tm-30) REVERT: D 306 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8836 (tm-30) REVERT: E 114 TRP cc_start: 0.7759 (m100) cc_final: 0.7357 (m100) outliers start: 3 outliers final: 0 residues processed: 121 average time/residue: 0.5270 time to fit residues: 96.0750 Evaluate side-chains 116 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 89 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN E 199 GLN E 410 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.064015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.054026 restraints weight = 130599.989| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.68 r_work: 0.2832 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 14020 Z= 0.253 Angle : 0.497 4.694 19085 Z= 0.269 Chirality : 0.041 0.144 2160 Planarity : 0.004 0.043 2375 Dihedral : 3.693 12.618 1955 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.13 % Allowed : 6.98 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.21), residues: 1670 helix: 3.20 (0.20), residues: 580 sheet: -0.59 (0.25), residues: 415 loop : -0.36 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 414 HIS 0.002 0.001 HIS B 105 PHE 0.011 0.002 PHE A 301 TYR 0.018 0.001 TYR B 297 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00037 ( 5) link_NAG-ASN : angle 1.12852 ( 15) hydrogen bonds : bond 0.03754 ( 710) hydrogen bonds : angle 4.67988 ( 2280) SS BOND : bond 0.00297 ( 5) SS BOND : angle 0.77621 ( 10) covalent geometry : bond 0.00547 (14010) covalent geometry : angle 0.49640 (19060) *********************** 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 115 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 2.176 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: 0.8444 (mm-40) cc_final: 0.8169 (mm110) REVERT: A 114 TRP cc_start: 0.7555 (m100) cc_final: 0.7162 (m100) REVERT: A 245 GLN cc_start: 0.8686 (mp10) cc_final: 0.8329 (tm-30) REVERT: B 114 TRP cc_start: 0.7757 (m100) cc_final: 0.7287 (m100) REVERT: B 306 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8907 (tm-30) REVERT: C 114 TRP cc_start: 0.7703 (m100) cc_final: 0.7289 (m100) REVERT: C 306 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8962 (tm-30) REVERT: D 114 TRP cc_start: 0.7604 (m100) cc_final: 0.7151 (m100) REVERT: D 216 MET cc_start: 0.8625 (mmm) cc_final: 0.7992 (mmm) REVERT: E 114 TRP cc_start: 0.7762 (m100) cc_final: 0.7320 (m100) REVERT: E 306 GLU cc_start: 0.9261 (tm-30) cc_final: 0.8865 (tm-30) outliers start: 2 outliers final: 2 residues processed: 114 average time/residue: 0.5149 time to fit residues: 90.5678 Evaluate side-chains 114 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 305 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN B 410 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.065870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.055704 restraints weight = 131625.113| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.77 r_work: 0.2848 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14020 Z= 0.107 Angle : 0.425 4.886 19085 Z= 0.222 Chirality : 0.040 0.181 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.398 12.483 1955 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.20 % Allowed : 6.85 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.21), residues: 1670 helix: 3.41 (0.20), residues: 610 sheet: -0.24 (0.28), residues: 380 loop : -0.33 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 414 HIS 0.002 0.001 HIS A 105 PHE 0.016 0.001 PHE A 301 TYR 0.012 0.001 TYR B 297 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 5) link_NAG-ASN : angle 1.03068 ( 15) hydrogen bonds : bond 0.03354 ( 710) hydrogen bonds : angle 4.34869 ( 2280) SS BOND : bond 0.00256 ( 5) SS BOND : angle 0.73645 ( 10) covalent geometry : bond 0.00226 (14010) covalent geometry : angle 0.42390 (19060) *********************** 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 127 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 1.954 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: 0.7585 (m100) cc_final: 0.7202 (m100) REVERT: A 216 MET cc_start: 0.8644 (mmm) cc_final: 0.8326 (mmm) REVERT: A 245 GLN cc_start: 0.8693 (mp10) cc_final: 0.8210 (tm-30) REVERT: B 60 GLU cc_start: 0.9215 (mp0) cc_final: 0.8740 (mp0) REVERT: B 114 TRP cc_start: 0.7830 (m100) cc_final: 0.7373 (m100) REVERT: B 216 MET cc_start: 0.8793 (mmm) cc_final: 0.8200 (mmm) REVERT: B 306 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8862 (tm-30) REVERT: C 85 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8215 (mm110) REVERT: C 114 TRP cc_start: 0.7699 (m100) cc_final: 0.7261 (m100) REVERT: C 232 GLN cc_start: 0.9378 (tp40) cc_final: 0.9167 (tp40) REVERT: C 306 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8890 (tm-30) REVERT: D 114 TRP cc_start: 0.7597 (m100) cc_final: 0.7155 (m100) REVERT: D 245 GLN cc_start: 0.8634 (mp10) cc_final: 0.8329 (tm-30) REVERT: E 114 TRP cc_start: 0.7771 (m100) cc_final: 0.7330 (m100) REVERT: E 306 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8856 (tm-30) outliers start: 3 outliers final: 2 residues processed: 126 average time/residue: 0.5132 time to fit residues: 97.2934 Evaluate side-chains 121 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 119 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain C residue 26 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 9 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN C 410 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.063775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.053873 restraints weight = 131771.430| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.68 r_work: 0.2828 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 14020 Z= 0.253 Angle : 0.493 4.675 19085 Z= 0.266 Chirality : 0.041 0.162 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.651 12.535 1955 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.07 % Allowed : 7.25 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1670 helix: 3.13 (0.20), residues: 610 sheet: -0.71 (0.24), residues: 440 loop : -0.46 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 174 HIS 0.003 0.001 HIS C 105 PHE 0.011 0.001 PHE A 301 TYR 0.014 0.001 TYR D 297 ARG 0.002 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00048 ( 5) link_NAG-ASN : angle 1.15443 ( 15) hydrogen bonds : bond 0.03612 ( 710) hydrogen bonds : angle 4.58154 ( 2280) SS BOND : bond 0.00290 ( 5) SS BOND : angle 0.76916 ( 10) covalent geometry : bond 0.00548 (14010) covalent geometry : angle 0.49200 (19060) *********************** 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 116 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 2.360 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: A 85 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8178 (mm110) REVERT: A 114 TRP cc_start: 0.7637 (m100) cc_final: 0.7238 (m100) REVERT: A 216 MET cc_start: 0.8732 (mmm) cc_final: 0.8414 (mmm) REVERT: A 245 GLN cc_start: 0.8687 (mp10) cc_final: 0.8327 (tm-30) REVERT: B 114 TRP cc_start: 0.7816 (m100) cc_final: 0.7352 (m100) REVERT: B 306 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8890 (tm-30) REVERT: C 114 TRP cc_start: 0.7750 (m100) cc_final: 0.7326 (m100) REVERT: C 306 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8927 (tm-30) REVERT: D 114 TRP cc_start: 0.7654 (m100) cc_final: 0.7218 (m100) REVERT: D 216 MET cc_start: 0.8618 (mmm) cc_final: 0.8032 (mmm) REVERT: D 245 GLN cc_start: 0.8660 (mp10) cc_final: 0.8325 (tm-30) REVERT: E 114 TRP cc_start: 0.7817 (m100) cc_final: 0.7376 (m100) REVERT: E 306 GLU cc_start: 0.9281 (tm-30) cc_final: 0.8873 (tm-30) outliers start: 1 outliers final: 1 residues processed: 116 average time/residue: 0.5697 time to fit residues: 100.0128 Evaluate side-chains 113 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 2.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 131 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.066686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.056228 restraints weight = 133948.695| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.85 r_work: 0.2857 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 14020 Z= 0.175 Angle : 0.453 4.755 19085 Z= 0.240 Chirality : 0.040 0.177 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.553 12.575 1955 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.13 % Allowed : 7.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.21), residues: 1670 helix: 3.22 (0.20), residues: 610 sheet: -0.55 (0.26), residues: 410 loop : -0.43 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 414 HIS 0.002 0.001 HIS C 105 PHE 0.013 0.001 PHE A 301 TYR 0.014 0.001 TYR D 297 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 5) link_NAG-ASN : angle 1.04161 ( 15) hydrogen bonds : bond 0.03457 ( 710) hydrogen bonds : angle 4.44918 ( 2280) SS BOND : bond 0.00270 ( 5) SS BOND : angle 0.77057 ( 10) covalent geometry : bond 0.00377 (14010) covalent geometry : angle 0.45162 (19060) *********************** 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 123 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 2.039 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: 0.8409 (mm-40) cc_final: 0.8158 (mm110) REVERT: A 114 TRP cc_start: 0.7602 (m100) cc_final: 0.7200 (m100) REVERT: A 245 GLN cc_start: 0.8694 (mp10) cc_final: 0.8329 (tm-30) REVERT: B 60 GLU cc_start: 0.9213 (mp0) cc_final: 0.8750 (mp0) REVERT: B 114 TRP cc_start: 0.7819 (m100) cc_final: 0.7348 (m100) REVERT: B 120 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8805 (mtt180) REVERT: B 306 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8900 (tm-30) REVERT: C 114 TRP cc_start: 0.7706 (m100) cc_final: 0.7277 (m100) REVERT: C 232 GLN cc_start: 0.9381 (tp40) cc_final: 0.9176 (tp40) REVERT: C 306 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8923 (tm-30) REVERT: D 114 TRP cc_start: 0.7610 (m100) cc_final: 0.7166 (m100) REVERT: D 216 MET cc_start: 0.8635 (mmm) cc_final: 0.8065 (mmm) REVERT: D 245 GLN cc_start: 0.8652 (mp10) cc_final: 0.8351 (tm-30) REVERT: E 114 TRP cc_start: 0.7788 (m100) cc_final: 0.7359 (m100) REVERT: E 306 GLU cc_start: 0.9271 (tm-30) cc_final: 0.8871 (tm-30) outliers start: 2 outliers final: 1 residues processed: 123 average time/residue: 0.5429 time to fit residues: 99.6832 Evaluate side-chains 122 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 120 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 120 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 57 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 overall best weight: 1.2788 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.066667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.056247 restraints weight = 130707.680| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.84 r_work: 0.2869 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14020 Z= 0.141 Angle : 0.443 4.908 19085 Z= 0.233 Chirality : 0.040 0.173 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.467 12.538 1955 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.20 % Allowed : 7.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.21), residues: 1670 helix: 3.31 (0.20), residues: 615 sheet: -0.30 (0.28), residues: 380 loop : -0.44 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 414 HIS 0.002 0.001 HIS C 105 PHE 0.012 0.001 PHE A 301 TYR 0.018 0.001 TYR B 297 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 5) link_NAG-ASN : angle 1.00905 ( 15) hydrogen bonds : bond 0.03365 ( 710) hydrogen bonds : angle 4.35205 ( 2280) SS BOND : bond 0.00255 ( 5) SS BOND : angle 0.75691 ( 10) covalent geometry : bond 0.00303 (14010) covalent geometry : angle 0.44194 (19060) ********************** 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 124 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 121 time to evaluate : 2.070 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: A 114 TRP cc_start: 0.7631 (m100) cc_final: 0.7234 (m100) REVERT: A 216 MET cc_start: 0.8669 (mmm) cc_final: 0.8399 (mmm) REVERT: A 239 MET cc_start: 0.8913 (mmm) cc_final: 0.8675 (mmt) REVERT: A 245 GLN cc_start: 0.8718 (mp10) cc_final: 0.8273 (tm-30) REVERT: B 60 GLU cc_start: 0.9206 (mp0) cc_final: 0.8722 (mp0) REVERT: B 114 TRP cc_start: 0.7846 (m100) cc_final: 0.7385 (m100) REVERT: B 120 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8820 (mtt180) REVERT: B 216 MET cc_start: 0.8828 (mmm) cc_final: 0.8260 (mmm) REVERT: B 245 GLN cc_start: 0.8764 (mp10) cc_final: 0.8322 (tm-30) REVERT: B 306 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8907 (tm-30) REVERT: C 114 TRP cc_start: 0.7675 (m100) cc_final: 0.7242 (m100) REVERT: C 232 GLN cc_start: 0.9373 (tp40) cc_final: 0.9171 (tp40) REVERT: C 306 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8935 (tm-30) REVERT: D 114 TRP cc_start: 0.7635 (m100) cc_final: 0.7202 (m100) REVERT: D 216 MET cc_start: 0.8623 (mmm) cc_final: 0.8066 (mmm) REVERT: D 245 GLN cc_start: 0.8651 (mp10) cc_final: 0.8343 (tm-30) REVERT: E 114 TRP cc_start: 0.7780 (m100) cc_final: 0.7333 (m100) REVERT: E 306 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8871 (tm-30) outliers start: 3 outliers final: 2 residues processed: 123 average time/residue: 0.5546 time to fit residues: 102.2750 Evaluate side-chains 123 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 120 ARG Chi-restraints excluded: chain C residue 26 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 117 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3277 r_free = 0.3277 target = 0.066185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.055835 restraints weight = 132978.358| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.62 r_work: 0.2870 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 14020 Z= 0.187 Angle : 0.466 4.738 19085 Z= 0.247 Chirality : 0.040 0.170 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.542 12.428 1955 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.13 % Allowed : 7.65 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.21), residues: 1670 helix: 3.21 (0.20), residues: 615 sheet: -0.56 (0.26), residues: 410 loop : -0.44 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 414 HIS 0.002 0.001 HIS C 105 PHE 0.012 0.001 PHE A 301 TYR 0.014 0.001 TYR E 297 ARG 0.002 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00041 ( 5) link_NAG-ASN : angle 1.06510 ( 15) hydrogen bonds : bond 0.03442 ( 710) hydrogen bonds : angle 4.43163 ( 2280) SS BOND : bond 0.00267 ( 5) SS BOND : angle 0.75325 ( 10) covalent geometry : bond 0.00404 (14010) covalent geometry : angle 0.46476 (19060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8779.57 seconds wall clock time: 152 minutes 24.73 seconds (9144.73 seconds total)