Starting phenix.real_space_refine on Mon Jun 23 16:17:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bej_16005/06_2025/8bej_16005_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bej_16005/06_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_16005/06_2025/8bej_16005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bej_16005/06_2025/8bej_16005.map" model { file = "/net/cci-nas-00/data/ceres_data/8bej_16005/06_2025/8bej_16005_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bej_16005/06_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-5710/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: 14.40, 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: 6.83 Conformation dependent library (CDL) restraints added in 1.9 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: 2.22 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: 10.13 Time building geometry restraints manager: 8.36 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: 0.12 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: 8.580 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: 0.490 Extract box with map and model: 1.160 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 58.120 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.180 ------------------------------------------------------------------------------- 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 : 2.134 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: 0.6802 time to fit residues: 176.9521 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 : 2.181 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.064179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.053941 restraints weight = 129460.502| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.72 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 : 2.247 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: 0.7538 (m100) cc_final: 0.7215 (m100) REVERT: B 61 MET cc_start: 0.8965 (mmm) cc_final: 0.8737 (tpp) REVERT: B 114 TRP cc_start: 0.7798 (m100) cc_final: 0.7448 (m100) REVERT: C 85 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8016 (mm110) REVERT: C 114 TRP cc_start: 0.7664 (m100) cc_final: 0.7310 (m100) REVERT: D 114 TRP cc_start: 0.7648 (m100) cc_final: 0.7263 (m100) REVERT: E 114 TRP cc_start: 0.7787 (m100) cc_final: 0.7403 (m100) outliers start: 8 outliers final: 6 residues processed: 145 average time/residue: 0.5885 time to fit residues: 128.4681 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 : 2.050 ------------------------------------------------------------------------------- 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: 1.9990 chunk 66 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 D 199 GLN E 199 GLN E 410 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.065593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.055252 restraints weight = 131063.221| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.77 r_work: 0.2847 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14020 Z= 0.159 Angle : 0.458 4.908 19085 Z= 0.244 Chirality : 0.040 0.143 2160 Planarity : 0.004 0.043 2375 Dihedral : 3.499 11.707 1955 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.07 % Allowed : 6.31 % Favored : 93.62 % 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: 1.52 (0.21), residues: 1670 helix: 3.00 (0.21), residues: 610 sheet: -0.04 (0.27), residues: 380 loop : -0.19 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 414 HIS 0.003 0.001 HIS A 105 PHE 0.008 0.001 PHE E 261 TYR 0.014 0.001 TYR B 297 ARG 0.002 0.000 ARG C 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 5) link_NAG-ASN : angle 0.98777 ( 15) hydrogen bonds : bond 0.04274 ( 710) hydrogen bonds : angle 4.91200 ( 2280) SS BOND : bond 0.00260 ( 5) SS BOND : angle 0.57706 ( 10) covalent geometry : bond 0.00336 (14010) covalent geometry : angle 0.45764 (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 : 1.969 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 85 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8162 (mm110) REVERT: A 114 TRP cc_start: 0.7509 (m100) cc_final: 0.7152 (m100) REVERT: B 85 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8261 (mm110) REVERT: B 114 TRP cc_start: 0.7763 (m100) cc_final: 0.7328 (m100) REVERT: C 85 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8069 (mm110) REVERT: C 114 TRP cc_start: 0.7669 (m100) cc_final: 0.7246 (m100) REVERT: D 114 TRP cc_start: 0.7578 (m100) cc_final: 0.7163 (m100) REVERT: D 245 GLN cc_start: 0.8607 (mp10) cc_final: 0.8313 (tm-30) REVERT: E 114 TRP cc_start: 0.7742 (m100) cc_final: 0.7342 (m100) REVERT: E 216 MET cc_start: 0.8754 (mmm) cc_final: 0.8153 (mmm) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.5647 time to fit residues: 110.2359 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 : 1.962 ------------------------------------------------------------------------------- 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: 2.9990 chunk 129 optimal weight: 3.9990 chunk 130 optimal weight: 0.0570 chunk 144 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN B 199 GLN C 199 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.067115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.056870 restraints weight = 130832.574| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 3.76 r_work: 0.2892 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14020 Z= 0.092 Angle : 0.427 4.253 19085 Z= 0.222 Chirality : 0.040 0.144 2160 Planarity : 0.004 0.045 2375 Dihedral : 3.305 12.105 1955 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.20 % Allowed : 5.03 % Favored : 94.77 % 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: 1.71 (0.21), residues: 1670 helix: 3.25 (0.20), residues: 610 sheet: 0.05 (0.27), residues: 380 loop : -0.17 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 414 HIS 0.002 0.001 HIS D 105 PHE 0.009 0.001 PHE A 301 TYR 0.016 0.001 TYR B 297 ARG 0.007 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 5) link_NAG-ASN : angle 1.00230 ( 15) hydrogen bonds : bond 0.03487 ( 710) hydrogen bonds : angle 4.43891 ( 2280) SS BOND : bond 0.00267 ( 5) SS BOND : angle 0.61293 ( 10) covalent geometry : bond 0.00194 (14010) covalent geometry : angle 0.42563 (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 130 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 127 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: A 114 TRP cc_start: 0.7472 (m100) cc_final: 0.7110 (m100) REVERT: A 245 GLN cc_start: 0.8680 (mp10) cc_final: 0.8257 (tm-30) REVERT: B 60 GLU cc_start: 0.9140 (mp0) cc_final: 0.8727 (mp0) REVERT: B 114 TRP cc_start: 0.7707 (m100) cc_final: 0.7255 (m100) REVERT: B 216 MET cc_start: 0.8719 (mmm) cc_final: 0.8241 (mmm) REVERT: C 85 GLN cc_start: 0.8331 (mm-40) cc_final: 0.8083 (mm110) REVERT: C 114 TRP cc_start: 0.7611 (m100) cc_final: 0.7182 (m100) REVERT: D 114 TRP cc_start: 0.7555 (m100) cc_final: 0.7127 (m100) REVERT: D 216 MET cc_start: 0.8601 (mmm) cc_final: 0.7981 (mmm) REVERT: D 245 GLN cc_start: 0.8606 (mp10) cc_final: 0.8318 (tm-30) REVERT: E 114 TRP cc_start: 0.7717 (m100) cc_final: 0.7319 (m100) outliers start: 3 outliers final: 0 residues processed: 129 average time/residue: 0.5631 time to fit residues: 110.2221 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 : 2.324 ------------------------------------------------------------------------------- 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: 3.9990 chunk 161 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 115 optimal weight: 0.0970 chunk 124 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 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 = 0.3250 r_free = 0.3250 target = 0.065756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.055463 restraints weight = 131280.476| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.74 r_work: 0.2853 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 14020 Z= 0.183 Angle : 0.457 4.541 19085 Z= 0.244 Chirality : 0.040 0.135 2160 Planarity : 0.004 0.043 2375 Dihedral : 3.463 12.575 1955 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.13 % Allowed : 6.31 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.55 (0.21), residues: 1670 helix: 3.22 (0.20), residues: 610 sheet: -0.12 (0.27), residues: 380 loop : -0.32 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 414 HIS 0.002 0.001 HIS D 105 PHE 0.022 0.001 PHE A 301 TYR 0.015 0.001 TYR B 297 ARG 0.004 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00033 ( 5) link_NAG-ASN : angle 1.06961 ( 15) hydrogen bonds : bond 0.03626 ( 710) hydrogen bonds : angle 4.50903 ( 2280) SS BOND : bond 0.00320 ( 5) SS BOND : angle 0.72404 ( 10) covalent geometry : bond 0.00395 (14010) covalent geometry : angle 0.45643 (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 117 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 2.411 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 114 TRP cc_start: 0.7583 (m100) cc_final: 0.7204 (m100) REVERT: A 245 GLN cc_start: 0.8711 (mp10) cc_final: 0.8291 (tm-30) REVERT: B 85 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8313 (mm110) REVERT: B 114 TRP cc_start: 0.7773 (m100) cc_final: 0.7323 (m100) REVERT: B 216 MET cc_start: 0.8762 (mmm) cc_final: 0.8263 (mmm) REVERT: B 306 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8908 (tm-30) REVERT: C 85 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8169 (mm110) REVERT: C 114 TRP cc_start: 0.7646 (m100) cc_final: 0.7212 (m100) REVERT: D 114 TRP cc_start: 0.7631 (m100) cc_final: 0.7189 (m100) REVERT: D 245 GLN cc_start: 0.8645 (mp10) cc_final: 0.8320 (tm-30) REVERT: E 114 TRP cc_start: 0.7768 (m100) cc_final: 0.7355 (m100) outliers start: 2 outliers final: 0 residues processed: 117 average time/residue: 0.7618 time to fit residues: 135.4213 Evaluate side-chains 115 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 4.479 ------------------------------------------------------------------------------- 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: 5.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 130 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.065927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.055576 restraints weight = 132304.767| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 3.73 r_work: 0.2855 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3575 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= 0.191 Angle : 0.459 4.918 19085 Z= 0.245 Chirality : 0.040 0.152 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.527 12.646 1955 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.27 % Allowed : 6.58 % Favored : 93.15 % 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: 1.47 (0.21), residues: 1670 helix: 3.26 (0.20), residues: 610 sheet: -0.27 (0.27), residues: 380 loop : -0.41 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 414 HIS 0.002 0.001 HIS D 105 PHE 0.012 0.001 PHE A 301 TYR 0.016 0.001 TYR B 297 ARG 0.004 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00053 ( 5) link_NAG-ASN : angle 1.04764 ( 15) hydrogen bonds : bond 0.03540 ( 710) hydrogen bonds : angle 4.49611 ( 2280) SS BOND : bond 0.00290 ( 5) SS BOND : angle 0.77461 ( 10) covalent geometry : bond 0.00410 (14010) covalent geometry : angle 0.45789 (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 123 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.8431 (mm-40) cc_final: 0.8173 (mm110) REVERT: A 114 TRP cc_start: 0.7523 (m100) cc_final: 0.7140 (m100) REVERT: A 216 MET cc_start: 0.8644 (mmm) cc_final: 0.8364 (mmm) REVERT: A 245 GLN cc_start: 0.8684 (mp10) cc_final: 0.8316 (tm-30) REVERT: B 60 GLU cc_start: 0.9182 (mp0) cc_final: 0.8732 (mp0) REVERT: B 85 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8337 (mm110) REVERT: B 114 TRP cc_start: 0.7766 (m100) cc_final: 0.7314 (m100) REVERT: B 306 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8895 (tm-30) REVERT: C 114 TRP cc_start: 0.7640 (m100) cc_final: 0.7209 (m100) REVERT: C 306 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8921 (tm-30) REVERT: D 85 GLN cc_start: 0.8553 (mm-40) cc_final: 0.8299 (mm110) REVERT: D 114 TRP cc_start: 0.7611 (m100) cc_final: 0.7157 (m100) REVERT: D 216 MET cc_start: 0.8634 (mmm) cc_final: 0.8068 (mmm) REVERT: D 245 GLN cc_start: 0.8633 (mp10) cc_final: 0.8322 (tm-30) REVERT: E 114 TRP cc_start: 0.7752 (m100) cc_final: 0.7325 (m100) REVERT: E 306 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8870 (tm-30) outliers start: 4 outliers final: 3 residues processed: 121 average time/residue: 0.5288 time to fit residues: 97.1183 Evaluate side-chains 118 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 SER Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain C residue 26 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 16 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.064524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.054571 restraints weight = 130907.936| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.74 r_work: 0.2844 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 14020 Z= 0.132 Angle : 0.432 4.514 19085 Z= 0.227 Chirality : 0.040 0.171 2160 Planarity : 0.004 0.043 2375 Dihedral : 3.408 12.599 1955 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.20 % Allowed : 6.64 % Favored : 93.15 % 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: 1.60 (0.21), residues: 1670 helix: 3.39 (0.20), residues: 610 sheet: -0.23 (0.28), residues: 380 loop : -0.34 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 414 HIS 0.002 0.001 HIS A 105 PHE 0.016 0.001 PHE A 301 TYR 0.015 0.001 TYR B 297 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00109 ( 5) link_NAG-ASN : angle 1.01704 ( 15) hydrogen bonds : bond 0.03360 ( 710) hydrogen bonds : angle 4.34106 ( 2280) SS BOND : bond 0.00266 ( 5) SS BOND : angle 0.73888 ( 10) covalent geometry : bond 0.00281 (14010) covalent geometry : angle 0.43095 (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 : 2.234 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 114 TRP cc_start: 0.7590 (m100) cc_final: 0.7205 (m100) REVERT: A 245 GLN cc_start: 0.8680 (mp10) cc_final: 0.8235 (tm-30) REVERT: B 60 GLU cc_start: 0.9206 (mp0) cc_final: 0.8722 (mp0) REVERT: B 114 TRP cc_start: 0.7839 (m100) cc_final: 0.7386 (m100) REVERT: B 216 MET cc_start: 0.8812 (mmm) cc_final: 0.8210 (mmm) REVERT: B 239 MET cc_start: 0.9186 (mmm) cc_final: 0.8961 (mmm) REVERT: B 306 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8871 (tm-30) REVERT: C 85 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8225 (mm110) REVERT: C 114 TRP cc_start: 0.7710 (m100) cc_final: 0.7273 (m100) REVERT: C 232 GLN cc_start: 0.9380 (tp40) cc_final: 0.9170 (tp40) REVERT: C 306 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8883 (tm-30) REVERT: D 114 TRP cc_start: 0.7643 (m100) cc_final: 0.7203 (m100) REVERT: D 245 GLN cc_start: 0.8637 (mp10) cc_final: 0.8310 (tm-30) REVERT: E 114 TRP cc_start: 0.7771 (m100) cc_final: 0.7346 (m100) REVERT: E 306 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8876 (tm-30) outliers start: 3 outliers final: 2 residues processed: 126 average time/residue: 0.5395 time to fit residues: 103.2088 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 : 1.946 ------------------------------------------------------------------------------- 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: 3.9990 chunk 144 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3230 r_free = 0.3230 target = 0.064556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.054351 restraints weight = 133754.015| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.69 r_work: 0.2855 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14020 Z= 0.201 Angle : 0.468 4.549 19085 Z= 0.249 Chirality : 0.040 0.165 2160 Planarity : 0.004 0.042 2375 Dihedral : 3.534 12.523 1955 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.27 % Allowed : 6.85 % 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: 1.41 (0.21), residues: 1670 helix: 3.29 (0.20), residues: 610 sheet: -0.38 (0.27), residues: 390 loop : -0.46 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 414 HIS 0.002 0.001 HIS D 105 PHE 0.011 0.001 PHE A 301 TYR 0.014 0.001 TYR B 297 ARG 0.002 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00032 ( 5) link_NAG-ASN : angle 1.08527 ( 15) hydrogen bonds : bond 0.03473 ( 710) hydrogen bonds : angle 4.45441 ( 2280) SS BOND : bond 0.00270 ( 5) SS BOND : angle 0.75619 ( 10) covalent geometry : bond 0.00435 (14010) covalent geometry : angle 0.46739 (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 122 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 2.020 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 85 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8181 (mm110) REVERT: A 114 TRP cc_start: 0.7593 (m100) cc_final: 0.7199 (m100) REVERT: A 216 MET cc_start: 0.8676 (mmm) cc_final: 0.8396 (mmm) REVERT: A 245 GLN cc_start: 0.8666 (mp10) cc_final: 0.8305 (tm-30) REVERT: B 60 GLU cc_start: 0.9192 (mp0) cc_final: 0.8720 (mp0) REVERT: B 85 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8319 (mm110) REVERT: B 114 TRP cc_start: 0.7810 (m100) cc_final: 0.7355 (m100) REVERT: B 216 MET cc_start: 0.8819 (mmm) cc_final: 0.8265 (mmm) REVERT: B 306 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8891 (tm-30) REVERT: C 114 TRP cc_start: 0.7722 (m100) cc_final: 0.7295 (m100) REVERT: C 306 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8909 (tm-30) REVERT: D 85 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8277 (mm110) REVERT: D 114 TRP cc_start: 0.7643 (m100) cc_final: 0.7220 (m100) REVERT: D 216 MET cc_start: 0.8611 (mmm) cc_final: 0.8084 (mmm) REVERT: D 245 GLN cc_start: 0.8651 (mp10) cc_final: 0.8315 (tm-30) REVERT: E 114 TRP cc_start: 0.7784 (m100) cc_final: 0.7364 (m100) REVERT: E 306 GLU cc_start: 0.9274 (tm-30) cc_final: 0.8885 (tm-30) outliers start: 4 outliers final: 2 residues processed: 121 average time/residue: 0.5383 time to fit residues: 98.2776 Evaluate side-chains 118 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain C residue 26 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 131 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 13 optimal weight: 0.0060 chunk 114 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 47 optimal weight: 0.0070 chunk 96 optimal weight: 0.8980 overall best weight: 0.4814 ------------------------------------------------------------------------------- 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 = 0.3265 r_free = 0.3265 target = 0.066373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.056256 restraints weight = 131492.270| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.76 r_work: 0.2874 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14020 Z= 0.089 Angle : 0.425 5.082 19085 Z= 0.220 Chirality : 0.040 0.176 2160 Planarity : 0.004 0.043 2375 Dihedral : 3.310 12.424 1955 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.13 % Allowed : 7.25 % Favored : 92.62 % 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: 1.74 (0.21), residues: 1670 helix: 3.51 (0.20), residues: 615 sheet: -0.16 (0.28), residues: 380 loop : -0.29 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 414 HIS 0.002 0.001 HIS B 195 PHE 0.014 0.001 PHE A 301 TYR 0.017 0.001 TYR D 297 ARG 0.003 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 5) link_NAG-ASN : angle 1.02942 ( 15) hydrogen bonds : bond 0.03177 ( 710) hydrogen bonds : angle 4.16039 ( 2280) SS BOND : bond 0.00222 ( 5) SS BOND : angle 0.75058 ( 10) covalent geometry : bond 0.00190 (14010) covalent geometry : angle 0.42420 (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 130 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 128 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 TRP cc_start: 0.7615 (m100) cc_final: 0.7224 (m100) REVERT: A 216 MET cc_start: 0.8624 (mmm) cc_final: 0.8344 (mmm) REVERT: A 245 GLN cc_start: 0.8691 (mp10) cc_final: 0.8237 (tm-30) REVERT: B 60 GLU cc_start: 0.9217 (mp0) cc_final: 0.8706 (mp0) REVERT: B 114 TRP cc_start: 0.7804 (m100) cc_final: 0.7376 (m100) REVERT: B 216 MET cc_start: 0.8776 (mmm) cc_final: 0.8180 (mmm) REVERT: B 245 GLN cc_start: 0.8737 (mp10) cc_final: 0.8320 (tm-30) REVERT: B 306 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8892 (tm-30) REVERT: C 114 TRP cc_start: 0.7656 (m100) cc_final: 0.7217 (m100) REVERT: C 216 MET cc_start: 0.8606 (mmm) cc_final: 0.8002 (mmm) REVERT: C 232 GLN cc_start: 0.9347 (tp40) cc_final: 0.9143 (tp40) REVERT: C 239 MET cc_start: 0.8865 (mmm) cc_final: 0.8553 (mmt) REVERT: C 306 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8895 (tm-30) REVERT: D 114 TRP cc_start: 0.7590 (m100) cc_final: 0.7162 (m100) REVERT: D 216 MET cc_start: 0.8631 (mmm) cc_final: 0.8082 (mmm) REVERT: D 245 GLN cc_start: 0.8650 (mp10) cc_final: 0.8339 (tm-30) REVERT: E 114 TRP cc_start: 0.7720 (m100) cc_final: 0.7282 (m100) REVERT: E 245 GLN cc_start: 0.8787 (mp10) cc_final: 0.8337 (tm-30) REVERT: E 306 GLU cc_start: 0.9257 (tm-30) cc_final: 0.8863 (tm-30) outliers start: 2 outliers final: 2 residues processed: 129 average time/residue: 0.5435 time to fit residues: 107.5025 Evaluate side-chains 125 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU 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 57 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 13 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.065550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.055328 restraints weight = 132312.444| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.78 r_work: 0.2840 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14020 Z= 0.151 Angle : 0.450 6.292 19085 Z= 0.235 Chirality : 0.040 0.162 2160 Planarity : 0.004 0.044 2375 Dihedral : 3.374 12.428 1955 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.13 % Allowed : 7.52 % 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: 1.63 (0.21), residues: 1670 helix: 3.43 (0.20), residues: 615 sheet: -0.21 (0.28), residues: 380 loop : -0.36 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 414 HIS 0.002 0.001 HIS B 105 PHE 0.010 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 0.00059 ( 5) link_NAG-ASN : angle 1.03408 ( 15) hydrogen bonds : bond 0.03290 ( 710) hydrogen bonds : angle 4.25817 ( 2280) SS BOND : bond 0.00263 ( 5) SS BOND : angle 0.75015 ( 10) covalent geometry : bond 0.00327 (14010) covalent geometry : angle 0.44909 (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: 2 poor density : 122 time to evaluate : 2.216 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: A 85 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8174 (mm110) REVERT: A 114 TRP cc_start: 0.7663 (m100) cc_final: 0.7251 (m100) REVERT: A 216 MET cc_start: 0.8676 (mmm) cc_final: 0.8364 (mmm) REVERT: A 245 GLN cc_start: 0.8717 (mp10) cc_final: 0.8234 (tm-30) REVERT: B 60 GLU cc_start: 0.9216 (mp0) cc_final: 0.8707 (mp0) REVERT: B 114 TRP cc_start: 0.7880 (m100) cc_final: 0.7459 (m100) REVERT: B 216 MET cc_start: 0.8803 (mmm) cc_final: 0.8214 (mmm) REVERT: B 245 GLN cc_start: 0.8754 (mp10) cc_final: 0.8307 (tm-30) REVERT: B 306 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8828 (tm-30) REVERT: C 114 TRP cc_start: 0.7717 (m100) cc_final: 0.7301 (m100) REVERT: C 216 MET cc_start: 0.8628 (mmm) cc_final: 0.8024 (mmm) REVERT: C 232 GLN cc_start: 0.9374 (tp40) cc_final: 0.9172 (tp40) REVERT: C 306 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8918 (tm-30) REVERT: D 114 TRP cc_start: 0.7676 (m100) cc_final: 0.7229 (m100) REVERT: D 216 MET cc_start: 0.8651 (mmm) cc_final: 0.8062 (mmm) REVERT: D 245 GLN cc_start: 0.8648 (mp10) cc_final: 0.8294 (tm-30) REVERT: E 114 TRP cc_start: 0.7786 (m100) cc_final: 0.7333 (m100) REVERT: E 245 GLN cc_start: 0.8795 (mp10) cc_final: 0.8333 (tm-30) REVERT: E 306 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8822 (tm-30) outliers start: 2 outliers final: 2 residues processed: 123 average time/residue: 0.5451 time to fit residues: 102.6672 Evaluate side-chains 124 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 122 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 LEU 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: 2.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 87 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.065400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.055715 restraints weight = 129399.616| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.57 r_work: 0.2893 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3914 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= 0.191 Angle : 0.476 7.719 19085 Z= 0.251 Chirality : 0.040 0.159 2160 Planarity : 0.004 0.044 2375 Dihedral : 3.519 12.505 1955 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.13 % Allowed : 7.58 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.44 (0.21), residues: 1670 helix: 3.32 (0.20), residues: 615 sheet: -0.37 (0.27), residues: 390 loop : -0.48 (0.22), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 414 HIS 0.002 0.001 HIS E 105 PHE 0.012 0.001 PHE B 301 TYR 0.013 0.001 TYR D 297 ARG 0.002 0.000 ARG A 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00039 ( 5) link_NAG-ASN : angle 1.07506 ( 15) hydrogen bonds : bond 0.03428 ( 710) hydrogen bonds : angle 4.38500 ( 2280) SS BOND : bond 0.00268 ( 5) SS BOND : angle 0.75541 ( 10) covalent geometry : bond 0.00413 (14010) covalent geometry : angle 0.47480 (19060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9881.47 seconds wall clock time: 172 minutes 29.48 seconds (10349.48 seconds total)