Starting phenix.real_space_refine on Thu Feb 5 20:46:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9md5_48168/02_2026/9md5_48168.cif Found real_map, /net/cci-nas-00/data/ceres_data/9md5_48168/02_2026/9md5_48168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9md5_48168/02_2026/9md5_48168.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9md5_48168/02_2026/9md5_48168.map" model { file = "/net/cci-nas-00/data/ceres_data/9md5_48168/02_2026/9md5_48168.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9md5_48168/02_2026/9md5_48168.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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 Ca 4 9.91 5 S 132 5.16 5 C 12416 2.51 5 N 3352 2.21 5 O 3976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19880 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3000 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 373} Chain: "H" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 996 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "B" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3000 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 373} Chain: "E" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 996 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "I" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "C" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3000 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 373} Chain: "F" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 996 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "J" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "D" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3000 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 11, 'TRANS': 373} Chain: "G" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 996 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "K" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "M" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "N" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "P" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' CA': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' CA': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' CA': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' CA': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.11, per 1000 atoms: 0.21 Number of scatterers: 19880 At special positions: 0 Unit cell: (144.275, 144.275, 82.65, 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) Ca 4 19.99 S 132 16.00 O 3976 8.00 N 3352 7.00 C 12416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.02 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.02 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 193 " distance=2.02 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=2.02 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.03 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " 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 ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " ALPHA1-6 " BMA M 3 " - " MAN M 6 " " BMA N 3 " - " MAN N 6 " " BMA O 3 " - " MAN O 6 " " BMA P 3 " - " MAN P 6 " BETA1-2 " MAN M 4 " - " NAG M 5 " " MAN N 4 " - " NAG N 5 " " MAN O 4 " - " NAG O 5 " " MAN P 4 " - " NAG P 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG A 501 " - " ASN A 146 " " NAG A 502 " - " ASN A 367 " " NAG A 504 " - " ASN A 93 " " NAG A 505 " - " ASN A 234 " " NAG A 506 " - " ASN A 309 " " NAG B 501 " - " ASN B 146 " " NAG B 502 " - " ASN B 367 " " NAG B 504 " - " ASN B 93 " " NAG B 505 " - " ASN B 234 " " NAG B 506 " - " ASN B 309 " " NAG C 501 " - " ASN C 146 " " NAG C 502 " - " ASN C 367 " " NAG C 504 " - " ASN C 93 " " NAG C 505 " - " ASN C 234 " " NAG C 506 " - " ASN C 309 " " NAG D 501 " - " ASN D 146 " " NAG D 502 " - " ASN D 367 " " NAG D 504 " - " ASN D 93 " " NAG D 505 " - " ASN D 234 " " NAG D 506 " - " ASN D 309 " " NAG M 1 " - " ASN A 200 " " NAG N 1 " - " ASN B 200 " " NAG O 1 " - " ASN C 200 " " NAG P 1 " - " ASN D 200 " Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 758.9 milliseconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4488 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 48 sheets defined 2.8% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.630A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.580A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.552A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.630A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.582A pdb=" N ASN B 146 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.552A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.630A pdb=" N ALA C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.582A pdb=" N ASN C 146 " --> pdb=" O GLY C 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.552A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.630A pdb=" N ALA D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.580A pdb=" N ASN D 146 " --> pdb=" O GLY D 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.552A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.516A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.766A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 133 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A 172 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.504A pdb=" N ASP A 213 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.825A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.743A pdb=" N THR A 252 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR A 267 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE A 254 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE A 256 " --> pdb=" O VAL A 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 283 removed outlier: 5.414A pdb=" N GLU A 277 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG A 292 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 355 removed outlier: 4.634A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU A 372 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL A 398 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR A 374 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL A 396 " --> pdb=" O TYR A 374 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR A 376 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG A 394 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.658A pdb=" N GLY H 10 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET H 34 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.658A pdb=" N GLY H 10 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR H 110 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N TYR H 100E" --> pdb=" O HIS H 96 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL H 98 " --> pdb=" O TYR H 100C" (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR H 100C" --> pdb=" O VAL H 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 5 removed outlier: 4.324A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.335A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU L 46 " --> pdb=" O ARG L 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 96 through 102 removed outlier: 3.516A pdb=" N GLY B 96 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL B 445 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.768A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 133 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.504A pdb=" N ASP B 213 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.824A pdb=" N VAL B 231 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 223 through 224 removed outlier: 7.743A pdb=" N THR B 252 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR B 267 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE B 254 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE B 265 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE B 256 " --> pdb=" O VAL B 263 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.430A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 352 through 355 removed outlier: 4.634A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY B 363 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LEU B 372 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL B 398 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR B 374 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N VAL B 396 " --> pdb=" O TYR B 374 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR B 376 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG B 394 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.658A pdb=" N GLY E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR E 110 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 12 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET E 34 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.658A pdb=" N GLY E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR E 110 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL E 12 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N TYR E 100E" --> pdb=" O HIS E 96 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL E 98 " --> pdb=" O TYR E 100C" (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR E 100C" --> pdb=" O VAL E 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 4 through 5 removed outlier: 4.324A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER I 67 " --> pdb=" O ASP I 70 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.334A pdb=" N MET I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE I 48 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU I 46 " --> pdb=" O ARG I 37 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 96 through 102 removed outlier: 3.516A pdb=" N GLY C 96 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL C 445 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LYS C 102 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG C 420 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.768A pdb=" N TRP C 115 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N THR C 138 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N THR C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN C 136 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA C 133 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG C 172 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 179 through 184 removed outlier: 3.504A pdb=" N ASP C 213 " --> pdb=" O PHE C 205 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR C 207 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 223 through 224 removed outlier: 3.825A pdb=" N VAL C 231 " --> pdb=" O THR C 238 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 223 through 224 removed outlier: 7.743A pdb=" N THR C 252 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR C 267 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE C 254 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE C 265 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE C 256 " --> pdb=" O VAL C 263 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 276 through 283 removed outlier: 5.426A pdb=" N GLU C 277 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG C 292 " --> pdb=" O GLU C 277 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 352 through 355 removed outlier: 4.633A pdb=" N TRP C 352 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY C 363 " --> pdb=" O TRP C 352 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU C 372 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL C 398 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR C 374 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL C 396 " --> pdb=" O TYR C 374 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR C 376 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG C 394 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.658A pdb=" N GLY F 10 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR F 110 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET F 34 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.658A pdb=" N GLY F 10 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR F 110 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL F 12 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N TYR F 100E" --> pdb=" O HIS F 96 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL F 98 " --> pdb=" O TYR F 100C" (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR F 100C" --> pdb=" O VAL F 98 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 4 through 5 removed outlier: 4.324A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER J 67 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.334A pdb=" N MET J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE J 48 " --> pdb=" O TRP J 35 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU J 46 " --> pdb=" O ARG J 37 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 96 through 102 removed outlier: 3.516A pdb=" N GLY D 96 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL D 445 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.766A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA D 133 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG D 172 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 179 through 184 removed outlier: 3.504A pdb=" N ASP D 213 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 223 through 224 removed outlier: 3.824A pdb=" N VAL D 231 " --> pdb=" O THR D 238 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 223 through 224 removed outlier: 7.742A pdb=" N THR D 252 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N THR D 267 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILE D 254 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE D 265 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N PHE D 256 " --> pdb=" O VAL D 263 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 276 through 283 removed outlier: 5.425A pdb=" N GLU D 277 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG D 292 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 352 through 355 removed outlier: 4.634A pdb=" N TRP D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY D 363 " --> pdb=" O TRP D 352 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N LEU D 372 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL D 398 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR D 374 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL D 396 " --> pdb=" O TYR D 374 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR D 376 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG D 394 " --> pdb=" O THR D 376 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.658A pdb=" N GLY G 10 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR G 110 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL G 12 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET G 34 " --> pdb=" O LYS G 50 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.658A pdb=" N GLY G 10 " --> pdb=" O THR G 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR G 110 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL G 12 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR G 100E" --> pdb=" O HIS G 96 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL G 98 " --> pdb=" O TYR G 100C" (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR G 100C" --> pdb=" O VAL G 98 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 4 through 5 removed outlier: 4.323A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER K 67 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.334A pdb=" N MET K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU K 46 " --> pdb=" O ARG K 37 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1500 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: 3.51 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6304 1.34 - 1.46: 5474 1.46 - 1.59: 8382 1.59 - 1.71: 0 1.71 - 1.83: 176 Bond restraints: 20336 Sorted by residual: bond pdb=" C GLY B 408 " pdb=" N ILE B 409 " ideal model delta sigma weight residual 1.329 1.297 0.032 2.31e-02 1.87e+03 1.94e+00 bond pdb=" C GLY A 408 " pdb=" N ILE A 409 " ideal model delta sigma weight residual 1.329 1.297 0.032 2.31e-02 1.87e+03 1.93e+00 bond pdb=" C GLY C 408 " pdb=" N ILE C 409 " ideal model delta sigma weight residual 1.329 1.297 0.032 2.31e-02 1.87e+03 1.93e+00 bond pdb=" C GLY D 408 " pdb=" N ILE D 409 " ideal model delta sigma weight residual 1.329 1.298 0.032 2.31e-02 1.87e+03 1.88e+00 bond pdb=" CB GLN G 39 " pdb=" CG GLN G 39 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.49e+00 ... (remaining 20331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 26972 2.18 - 4.37: 521 4.37 - 6.55: 67 6.55 - 8.74: 0 8.74 - 10.92: 12 Bond angle restraints: 27572 Sorted by residual: angle pdb=" C ASP F 99 " pdb=" N GLU F 100 " pdb=" CA GLU F 100 " ideal model delta sigma weight residual 121.54 131.37 -9.83 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C ASP E 99 " pdb=" N GLU E 100 " pdb=" CA GLU E 100 " ideal model delta sigma weight residual 121.54 131.35 -9.81 1.91e+00 2.74e-01 2.64e+01 angle pdb=" C ASP H 99 " pdb=" N GLU H 100 " pdb=" CA GLU H 100 " ideal model delta sigma weight residual 121.54 131.10 -9.56 1.91e+00 2.74e-01 2.51e+01 angle pdb=" C ASP G 99 " pdb=" N GLU G 100 " pdb=" CA GLU G 100 " ideal model delta sigma weight residual 121.54 131.01 -9.47 1.91e+00 2.74e-01 2.46e+01 angle pdb=" N VAL G 98 " pdb=" CA VAL G 98 " pdb=" C VAL G 98 " ideal model delta sigma weight residual 109.29 103.44 5.85 1.42e+00 4.96e-01 1.70e+01 ... (remaining 27567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.55: 11033 14.55 - 29.10: 1095 29.10 - 43.65: 336 43.65 - 58.20: 76 58.20 - 72.75: 36 Dihedral angle restraints: 12576 sinusoidal: 5516 harmonic: 7060 Sorted by residual: dihedral pdb=" CA CYS B 417 " pdb=" C CYS B 417 " pdb=" N ILE B 418 " pdb=" CA ILE B 418 " ideal model delta harmonic sigma weight residual 180.00 148.02 31.98 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA CYS C 417 " pdb=" C CYS C 417 " pdb=" N ILE C 418 " pdb=" CA ILE C 418 " ideal model delta harmonic sigma weight residual 180.00 148.02 31.98 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CA CYS D 417 " pdb=" C CYS D 417 " pdb=" N ILE D 418 " pdb=" CA ILE D 418 " ideal model delta harmonic sigma weight residual 180.00 148.02 31.98 0 5.00e+00 4.00e-02 4.09e+01 ... (remaining 12573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 3034 0.126 - 0.252: 58 0.252 - 0.378: 0 0.378 - 0.504: 0 0.504 - 0.630: 4 Chirality restraints: 3096 Sorted by residual: chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN C 200 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.93e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 200 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.93e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN D 200 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.89e+00 ... (remaining 3093 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP G 99 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C ASP G 99 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP G 99 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU G 100 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 99 " 0.009 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C ASP H 99 " -0.033 2.00e-02 2.50e+03 pdb=" O ASP H 99 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU H 100 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 99 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C ASP F 99 " 0.033 2.00e-02 2.50e+03 pdb=" O ASP F 99 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU F 100 " -0.011 2.00e-02 2.50e+03 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 803 2.70 - 3.25: 18839 3.25 - 3.80: 33599 3.80 - 4.35: 46770 4.35 - 4.90: 79158 Nonbonded interactions: 179169 Sorted by model distance: nonbonded pdb=" O ALA C 246 " pdb=" ND2 ASN C 294 " model vdw 2.144 3.120 nonbonded pdb=" NH1 ARG C 152 " pdb=" OD2 ASP C 198 " model vdw 2.180 3.120 nonbonded pdb=" NH1 ARG B 152 " pdb=" OD2 ASP B 198 " model vdw 2.180 3.120 nonbonded pdb=" NH1 ARG D 152 " pdb=" OD2 ASP D 198 " model vdw 2.192 3.120 nonbonded pdb=" NH1 ARG A 152 " pdb=" OD2 ASP A 198 " model vdw 2.192 3.120 ... (remaining 179164 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'L' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 6.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.980 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 : 0.006 0.047 20424 Z= 0.258 Angle : 0.808 16.226 27792 Z= 0.406 Chirality : 0.056 0.630 3096 Planarity : 0.005 0.056 3468 Dihedral : 13.206 72.747 7956 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.64 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.16), residues: 2448 helix: -4.56 (0.28), residues: 24 sheet: -0.61 (0.17), residues: 960 loop : -1.52 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 100A TYR 0.019 0.002 TYR B 121 PHE 0.022 0.002 PHE F 100F TRP 0.021 0.002 TRP F 100D HIS 0.004 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00597 (20336) covalent geometry : angle 0.75709 (27572) SS BOND : bond 0.00438 ( 44) SS BOND : angle 2.09151 ( 88) hydrogen bonds : bond 0.21566 ( 556) hydrogen bonds : angle 11.17421 ( 1500) link_ALPHA1-3 : bond 0.00858 ( 4) link_ALPHA1-3 : angle 2.53173 ( 12) link_ALPHA1-6 : bond 0.00660 ( 4) link_ALPHA1-6 : angle 1.46262 ( 12) link_BETA1-2 : bond 0.00763 ( 4) link_BETA1-2 : angle 1.91822 ( 12) link_BETA1-4 : bond 0.00694 ( 8) link_BETA1-4 : angle 2.57436 ( 24) link_NAG-ASN : bond 0.00591 ( 24) link_NAG-ASN : angle 4.78785 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.572 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.4377 time to fit residues: 144.5035 Evaluate side-chains 236 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 441 ASN B 294 ASN B 441 ASN C 441 ASN D 441 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.152088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123276 restraints weight = 22687.797| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.65 r_work: 0.3293 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20424 Z= 0.149 Angle : 0.674 13.434 27792 Z= 0.343 Chirality : 0.051 0.547 3096 Planarity : 0.004 0.042 3468 Dihedral : 7.924 55.852 3604 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.74 % Favored : 95.10 % Rotamer: Outliers : 1.96 % Allowed : 7.65 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.16), residues: 2448 helix: -3.28 (0.77), residues: 24 sheet: -0.52 (0.16), residues: 940 loop : -1.43 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 152 TYR 0.022 0.002 TYR A 121 PHE 0.012 0.002 PHE B 410 TRP 0.011 0.001 TRP D 218 HIS 0.002 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00326 (20336) covalent geometry : angle 0.63162 (27572) SS BOND : bond 0.00300 ( 44) SS BOND : angle 1.45197 ( 88) hydrogen bonds : bond 0.04517 ( 556) hydrogen bonds : angle 8.32571 ( 1500) link_ALPHA1-3 : bond 0.01262 ( 4) link_ALPHA1-3 : angle 1.78100 ( 12) link_ALPHA1-6 : bond 0.00920 ( 4) link_ALPHA1-6 : angle 1.39647 ( 12) link_BETA1-2 : bond 0.00650 ( 4) link_BETA1-2 : angle 1.14735 ( 12) link_BETA1-4 : bond 0.00744 ( 8) link_BETA1-4 : angle 2.30542 ( 24) link_NAG-ASN : bond 0.00647 ( 24) link_NAG-ASN : angle 4.11720 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 287 time to evaluate : 0.772 Fit side-chains REVERT: A 128 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7604 (mtpp) REVERT: A 199 ASN cc_start: 0.7532 (m-40) cc_final: 0.7047 (m-40) REVERT: A 339 ASP cc_start: 0.8264 (m-30) cc_final: 0.7918 (p0) REVERT: B 128 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7610 (mtpp) REVERT: B 199 ASN cc_start: 0.7522 (m-40) cc_final: 0.7038 (m-40) REVERT: B 339 ASP cc_start: 0.8297 (m-30) cc_final: 0.7939 (p0) REVERT: C 128 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7611 (mtpp) REVERT: C 199 ASN cc_start: 0.7519 (m-40) cc_final: 0.7032 (m-40) REVERT: C 339 ASP cc_start: 0.8299 (m-30) cc_final: 0.7938 (p0) REVERT: D 128 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7591 (mtpp) REVERT: D 199 ASN cc_start: 0.7534 (m-40) cc_final: 0.7053 (m-40) REVERT: D 339 ASP cc_start: 0.8301 (m-30) cc_final: 0.7932 (p0) outliers start: 42 outliers final: 16 residues processed: 304 average time/residue: 0.4531 time to fit residues: 161.8285 Evaluate side-chains 271 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 251 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 128 LYS Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain D residue 128 LYS Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 93 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 17 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 441 ASN B 441 ASN C 441 ASN D 441 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.152945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124310 restraints weight = 22701.397| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.65 r_work: 0.3303 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20424 Z= 0.133 Angle : 0.625 13.028 27792 Z= 0.315 Chirality : 0.050 0.531 3096 Planarity : 0.004 0.041 3468 Dihedral : 7.493 56.217 3604 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.21 % Favored : 95.63 % Rotamer: Outliers : 2.52 % Allowed : 10.82 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.16), residues: 2448 helix: -2.69 (1.01), residues: 24 sheet: -0.42 (0.16), residues: 924 loop : -1.26 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 292 TYR 0.018 0.002 TYR B 121 PHE 0.012 0.002 PHE F 100F TRP 0.011 0.001 TRP C 178 HIS 0.002 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00293 (20336) covalent geometry : angle 0.58494 (27572) SS BOND : bond 0.00196 ( 44) SS BOND : angle 1.00383 ( 88) hydrogen bonds : bond 0.03925 ( 556) hydrogen bonds : angle 7.46835 ( 1500) link_ALPHA1-3 : bond 0.01211 ( 4) link_ALPHA1-3 : angle 1.78022 ( 12) link_ALPHA1-6 : bond 0.00972 ( 4) link_ALPHA1-6 : angle 1.37849 ( 12) link_BETA1-2 : bond 0.00590 ( 4) link_BETA1-2 : angle 1.12204 ( 12) link_BETA1-4 : bond 0.00767 ( 8) link_BETA1-4 : angle 2.33711 ( 24) link_NAG-ASN : bond 0.00629 ( 24) link_NAG-ASN : angle 3.96949 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 251 time to evaluate : 0.680 Fit side-chains REVERT: A 199 ASN cc_start: 0.7470 (m-40) cc_final: 0.7034 (m-40) REVERT: A 339 ASP cc_start: 0.8255 (m-30) cc_final: 0.7917 (p0) REVERT: B 199 ASN cc_start: 0.7458 (m-40) cc_final: 0.7025 (m-40) REVERT: B 294 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8648 (t0) REVERT: B 339 ASP cc_start: 0.8255 (m-30) cc_final: 0.7928 (p0) REVERT: C 199 ASN cc_start: 0.7463 (m-40) cc_final: 0.7028 (m-40) REVERT: C 339 ASP cc_start: 0.8268 (m-30) cc_final: 0.7926 (p0) REVERT: D 199 ASN cc_start: 0.7470 (m-40) cc_final: 0.7035 (m-40) REVERT: D 339 ASP cc_start: 0.8267 (m-30) cc_final: 0.7925 (p0) outliers start: 54 outliers final: 18 residues processed: 286 average time/residue: 0.4487 time to fit residues: 149.8449 Evaluate side-chains 254 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 93 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 150 optimal weight: 0.4980 chunk 217 optimal weight: 0.0980 chunk 235 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 166 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN A 441 ASN B 141 ASN B 294 ASN B 441 ASN C 141 ASN C 441 ASN F 39 GLN J 38 GLN D 141 ASN D 441 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122071 restraints weight = 22847.018| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.65 r_work: 0.3274 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20424 Z= 0.171 Angle : 0.642 13.647 27792 Z= 0.322 Chirality : 0.051 0.554 3096 Planarity : 0.004 0.041 3468 Dihedral : 7.472 56.696 3604 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.58 % Favored : 95.26 % Rotamer: Outliers : 2.52 % Allowed : 13.25 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.16), residues: 2448 helix: -2.57 (1.07), residues: 24 sheet: -0.38 (0.16), residues: 916 loop : -1.22 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 172 TYR 0.017 0.002 TYR B 121 PHE 0.014 0.002 PHE F 100F TRP 0.012 0.001 TRP C 178 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00391 (20336) covalent geometry : angle 0.59930 (27572) SS BOND : bond 0.00322 ( 44) SS BOND : angle 1.04593 ( 88) hydrogen bonds : bond 0.03651 ( 556) hydrogen bonds : angle 7.20411 ( 1500) link_ALPHA1-3 : bond 0.01093 ( 4) link_ALPHA1-3 : angle 1.99172 ( 12) link_ALPHA1-6 : bond 0.00891 ( 4) link_ALPHA1-6 : angle 1.41473 ( 12) link_BETA1-2 : bond 0.00613 ( 4) link_BETA1-2 : angle 1.29029 ( 12) link_BETA1-4 : bond 0.00702 ( 8) link_BETA1-4 : angle 2.46318 ( 24) link_NAG-ASN : bond 0.00620 ( 24) link_NAG-ASN : angle 4.08494 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 244 time to evaluate : 0.902 Fit side-chains REVERT: A 131 GLN cc_start: 0.8644 (tt0) cc_final: 0.8351 (pt0) REVERT: A 199 ASN cc_start: 0.7584 (m-40) cc_final: 0.7141 (m-40) REVERT: A 339 ASP cc_start: 0.8216 (m-30) cc_final: 0.7895 (p0) REVERT: B 131 GLN cc_start: 0.8682 (tt0) cc_final: 0.8414 (pt0) REVERT: B 199 ASN cc_start: 0.7581 (m-40) cc_final: 0.7143 (m-40) REVERT: B 339 ASP cc_start: 0.8237 (m-30) cc_final: 0.7905 (p0) REVERT: C 131 GLN cc_start: 0.8684 (tt0) cc_final: 0.8418 (pt0) REVERT: C 199 ASN cc_start: 0.7573 (m-40) cc_final: 0.7134 (m-40) REVERT: C 339 ASP cc_start: 0.8239 (m-30) cc_final: 0.7898 (p0) REVERT: D 131 GLN cc_start: 0.8649 (tt0) cc_final: 0.8354 (pt0) REVERT: D 199 ASN cc_start: 0.7585 (m-40) cc_final: 0.7140 (m-40) REVERT: D 339 ASP cc_start: 0.8237 (m-30) cc_final: 0.7897 (p0) outliers start: 54 outliers final: 26 residues processed: 276 average time/residue: 0.4951 time to fit residues: 160.5401 Evaluate side-chains 258 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 117 optimal weight: 5.9990 chunk 110 optimal weight: 0.3980 chunk 209 optimal weight: 0.4980 chunk 163 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 chunk 225 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 ASN C 274 HIS C 441 ASN D 441 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.152633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.123912 restraints weight = 22784.602| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.65 r_work: 0.3299 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20424 Z= 0.126 Angle : 0.609 12.730 27792 Z= 0.305 Chirality : 0.050 0.525 3096 Planarity : 0.004 0.042 3468 Dihedral : 7.174 56.187 3604 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.04 % Favored : 95.79 % Rotamer: Outliers : 2.85 % Allowed : 13.67 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.16), residues: 2448 helix: -2.61 (1.04), residues: 24 sheet: -0.36 (0.16), residues: 916 loop : -1.15 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 118 TYR 0.014 0.001 TYR D 121 PHE 0.011 0.001 PHE H 100F TRP 0.012 0.001 TRP C 178 HIS 0.002 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00277 (20336) covalent geometry : angle 0.57108 (27572) SS BOND : bond 0.00179 ( 44) SS BOND : angle 0.82163 ( 88) hydrogen bonds : bond 0.03362 ( 556) hydrogen bonds : angle 6.91848 ( 1500) link_ALPHA1-3 : bond 0.01244 ( 4) link_ALPHA1-3 : angle 1.72653 ( 12) link_ALPHA1-6 : bond 0.01001 ( 4) link_ALPHA1-6 : angle 1.40984 ( 12) link_BETA1-2 : bond 0.00611 ( 4) link_BETA1-2 : angle 1.07250 ( 12) link_BETA1-4 : bond 0.00778 ( 8) link_BETA1-4 : angle 2.25556 ( 24) link_NAG-ASN : bond 0.00622 ( 24) link_NAG-ASN : angle 3.85560 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 240 time to evaluate : 0.821 Fit side-chains REVERT: A 199 ASN cc_start: 0.7500 (m-40) cc_final: 0.7080 (m-40) REVERT: A 339 ASP cc_start: 0.8183 (m-30) cc_final: 0.7869 (p0) REVERT: B 199 ASN cc_start: 0.7494 (m-40) cc_final: 0.7088 (m-40) REVERT: B 339 ASP cc_start: 0.8207 (m-30) cc_final: 0.7877 (p0) REVERT: C 199 ASN cc_start: 0.7490 (m-40) cc_final: 0.7084 (m-40) REVERT: C 339 ASP cc_start: 0.8182 (m-30) cc_final: 0.7852 (p0) REVERT: D 199 ASN cc_start: 0.7523 (m-40) cc_final: 0.7102 (m-40) REVERT: D 339 ASP cc_start: 0.8192 (m-30) cc_final: 0.7863 (p0) outliers start: 61 outliers final: 40 residues processed: 279 average time/residue: 0.4185 time to fit residues: 139.9793 Evaluate side-chains 273 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain E residue 2 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 93 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 230 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 172 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 140 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN B 131 GLN C 131 GLN C 141 ASN C 274 HIS C 441 ASN D 131 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.146444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.117109 restraints weight = 23022.289| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.67 r_work: 0.3226 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 20424 Z= 0.244 Angle : 0.692 15.336 27792 Z= 0.346 Chirality : 0.054 0.609 3096 Planarity : 0.004 0.043 3468 Dihedral : 7.736 57.451 3604 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.39 % Favored : 94.44 % Rotamer: Outliers : 2.80 % Allowed : 13.95 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.16), residues: 2448 helix: -2.62 (1.09), residues: 24 sheet: -0.35 (0.16), residues: 896 loop : -1.21 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 118 TYR 0.016 0.002 TYR A 121 PHE 0.018 0.002 PHE F 100F TRP 0.012 0.002 TRP B 178 HIS 0.003 0.001 HIS C 184 Details of bonding type rmsd covalent geometry : bond 0.00569 (20336) covalent geometry : angle 0.64250 (27572) SS BOND : bond 0.00384 ( 44) SS BOND : angle 1.40793 ( 88) hydrogen bonds : bond 0.03759 ( 556) hydrogen bonds : angle 7.05665 ( 1500) link_ALPHA1-3 : bond 0.00901 ( 4) link_ALPHA1-3 : angle 2.46388 ( 12) link_ALPHA1-6 : bond 0.00705 ( 4) link_ALPHA1-6 : angle 1.49432 ( 12) link_BETA1-2 : bond 0.00527 ( 4) link_BETA1-2 : angle 1.55440 ( 12) link_BETA1-4 : bond 0.00690 ( 8) link_BETA1-4 : angle 2.76736 ( 24) link_NAG-ASN : bond 0.00661 ( 24) link_NAG-ASN : angle 4.47993 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 236 time to evaluate : 0.824 Fit side-chains REVERT: A 339 ASP cc_start: 0.8265 (m-30) cc_final: 0.7864 (p0) REVERT: H 81 GLN cc_start: 0.7270 (tt0) cc_final: 0.6989 (tp-100) REVERT: B 339 ASP cc_start: 0.8282 (m-30) cc_final: 0.7879 (p0) REVERT: E 81 GLN cc_start: 0.7280 (tt0) cc_final: 0.7000 (tp-100) REVERT: C 339 ASP cc_start: 0.8301 (m-30) cc_final: 0.7881 (p0) REVERT: F 81 GLN cc_start: 0.7269 (tt0) cc_final: 0.6989 (tp-100) REVERT: D 339 ASP cc_start: 0.8270 (m-30) cc_final: 0.7869 (p0) REVERT: G 81 GLN cc_start: 0.7277 (tt0) cc_final: 0.6996 (tp-100) outliers start: 60 outliers final: 38 residues processed: 266 average time/residue: 0.4460 time to fit residues: 141.7971 Evaluate side-chains 274 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 93 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 224 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 166 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 294 ASN B 441 ASN C 141 ASN C 441 ASN J 38 GLN D 441 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.151222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122643 restraints weight = 22870.645| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.65 r_work: 0.3282 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20424 Z= 0.130 Angle : 0.616 12.983 27792 Z= 0.309 Chirality : 0.050 0.527 3096 Planarity : 0.004 0.043 3468 Dihedral : 7.271 55.798 3604 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.24 % Rotamer: Outliers : 2.85 % Allowed : 14.27 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.16), residues: 2448 helix: -2.72 (1.03), residues: 24 sheet: -0.23 (0.17), residues: 892 loop : -1.10 (0.16), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 118 TYR 0.013 0.001 TYR A 121 PHE 0.011 0.002 PHE B 354 TRP 0.014 0.001 TRP A 178 HIS 0.002 0.001 HIS B 168 Details of bonding type rmsd covalent geometry : bond 0.00284 (20336) covalent geometry : angle 0.57681 (27572) SS BOND : bond 0.00208 ( 44) SS BOND : angle 0.95268 ( 88) hydrogen bonds : bond 0.03290 ( 556) hydrogen bonds : angle 6.72205 ( 1500) link_ALPHA1-3 : bond 0.01247 ( 4) link_ALPHA1-3 : angle 1.74557 ( 12) link_ALPHA1-6 : bond 0.00965 ( 4) link_ALPHA1-6 : angle 1.42606 ( 12) link_BETA1-2 : bond 0.00617 ( 4) link_BETA1-2 : angle 1.03591 ( 12) link_BETA1-4 : bond 0.00794 ( 8) link_BETA1-4 : angle 2.27945 ( 24) link_NAG-ASN : bond 0.00616 ( 24) link_NAG-ASN : angle 3.89935 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 237 time to evaluate : 0.843 Fit side-chains REVERT: A 339 ASP cc_start: 0.8202 (m-30) cc_final: 0.7857 (p0) REVERT: H 81 GLN cc_start: 0.7258 (tt0) cc_final: 0.6911 (tp-100) REVERT: B 339 ASP cc_start: 0.8202 (m-30) cc_final: 0.7836 (p0) REVERT: B 443 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7834 (mt) REVERT: E 81 GLN cc_start: 0.7242 (tt0) cc_final: 0.6898 (tp-100) REVERT: C 339 ASP cc_start: 0.8190 (m-30) cc_final: 0.7821 (p0) REVERT: F 81 GLN cc_start: 0.7238 (tt0) cc_final: 0.6902 (tp-100) REVERT: D 339 ASP cc_start: 0.8211 (m-30) cc_final: 0.7855 (p0) REVERT: D 443 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7835 (mt) REVERT: G 81 GLN cc_start: 0.7261 (tt0) cc_final: 0.6913 (tp-100) outliers start: 61 outliers final: 31 residues processed: 274 average time/residue: 0.4036 time to fit residues: 133.9375 Evaluate side-chains 270 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 203 optimal weight: 0.6980 chunk 175 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 18 optimal weight: 0.0370 chunk 148 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 441 ASN B 173 GLN B 294 ASN B 441 ASN C 141 ASN C 173 GLN C 274 HIS C 441 ASN D 173 GLN D 441 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.151979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123440 restraints weight = 22801.307| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.66 r_work: 0.3295 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20424 Z= 0.127 Angle : 0.612 12.692 27792 Z= 0.305 Chirality : 0.050 0.527 3096 Planarity : 0.003 0.043 3468 Dihedral : 7.028 56.163 3604 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.41 % Favored : 95.42 % Rotamer: Outliers : 2.85 % Allowed : 14.09 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.17), residues: 2448 helix: -2.68 (1.04), residues: 24 sheet: -0.27 (0.17), residues: 920 loop : -0.99 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 118 TYR 0.018 0.002 TYR E 58 PHE 0.011 0.002 PHE D 354 TRP 0.012 0.001 TRP B 178 HIS 0.002 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00282 (20336) covalent geometry : angle 0.57409 (27572) SS BOND : bond 0.00191 ( 44) SS BOND : angle 0.86113 ( 88) hydrogen bonds : bond 0.03238 ( 556) hydrogen bonds : angle 6.55832 ( 1500) link_ALPHA1-3 : bond 0.01202 ( 4) link_ALPHA1-3 : angle 1.78643 ( 12) link_ALPHA1-6 : bond 0.00999 ( 4) link_ALPHA1-6 : angle 1.43194 ( 12) link_BETA1-2 : bond 0.00568 ( 4) link_BETA1-2 : angle 1.07236 ( 12) link_BETA1-4 : bond 0.00757 ( 8) link_BETA1-4 : angle 2.26999 ( 24) link_NAG-ASN : bond 0.00606 ( 24) link_NAG-ASN : angle 3.82656 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 241 time to evaluate : 0.831 Fit side-chains REVERT: A 199 ASN cc_start: 0.7473 (m-40) cc_final: 0.7044 (m-40) REVERT: A 339 ASP cc_start: 0.8177 (m-30) cc_final: 0.7820 (p0) REVERT: B 199 ASN cc_start: 0.7480 (m-40) cc_final: 0.7054 (m-40) REVERT: B 339 ASP cc_start: 0.8178 (m-30) cc_final: 0.7822 (p0) REVERT: B 389 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8312 (mttm) REVERT: C 199 ASN cc_start: 0.7474 (m-40) cc_final: 0.7046 (m-40) REVERT: C 339 ASP cc_start: 0.8173 (m-30) cc_final: 0.7806 (p0) REVERT: C 389 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8313 (mttm) REVERT: F 81 GLN cc_start: 0.7238 (tt0) cc_final: 0.6923 (tp-100) REVERT: D 199 ASN cc_start: 0.7476 (m-40) cc_final: 0.7049 (m-40) REVERT: D 339 ASP cc_start: 0.8161 (m-30) cc_final: 0.7803 (p0) outliers start: 61 outliers final: 37 residues processed: 275 average time/residue: 0.3807 time to fit residues: 127.0046 Evaluate side-chains 274 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 389 LYS Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 389 LYS Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 93 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 45 optimal weight: 0.9980 chunk 229 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 238 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 230 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.151258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122947 restraints weight = 22652.034| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.63 r_work: 0.3281 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20424 Z= 0.148 Angle : 0.631 13.070 27792 Z= 0.313 Chirality : 0.051 0.541 3096 Planarity : 0.004 0.042 3468 Dihedral : 7.013 56.359 3604 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.76 % Favored : 96.08 % Rotamer: Outliers : 2.71 % Allowed : 14.41 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.17), residues: 2448 helix: -2.70 (1.04), residues: 24 sheet: -0.27 (0.17), residues: 932 loop : -1.00 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 118 TYR 0.013 0.002 TYR J 49 PHE 0.013 0.002 PHE E 100F TRP 0.014 0.001 TRP H 100D HIS 0.002 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00335 (20336) covalent geometry : angle 0.59293 (27572) SS BOND : bond 0.00225 ( 44) SS BOND : angle 0.88407 ( 88) hydrogen bonds : bond 0.03309 ( 556) hydrogen bonds : angle 6.55283 ( 1500) link_ALPHA1-3 : bond 0.01156 ( 4) link_ALPHA1-3 : angle 1.89600 ( 12) link_ALPHA1-6 : bond 0.00952 ( 4) link_ALPHA1-6 : angle 1.43480 ( 12) link_BETA1-2 : bond 0.00554 ( 4) link_BETA1-2 : angle 1.16350 ( 12) link_BETA1-4 : bond 0.00732 ( 8) link_BETA1-4 : angle 2.30579 ( 24) link_NAG-ASN : bond 0.00598 ( 24) link_NAG-ASN : angle 3.91261 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 243 time to evaluate : 0.676 Fit side-chains REVERT: A 199 ASN cc_start: 0.7521 (m-40) cc_final: 0.7097 (m-40) REVERT: A 339 ASP cc_start: 0.8187 (m-30) cc_final: 0.7834 (p0) REVERT: A 443 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7830 (mt) REVERT: H 81 GLN cc_start: 0.7250 (tt0) cc_final: 0.6924 (tp-100) REVERT: B 199 ASN cc_start: 0.7530 (m-40) cc_final: 0.7101 (m-40) REVERT: B 339 ASP cc_start: 0.8195 (m-30) cc_final: 0.7840 (p0) REVERT: B 443 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7838 (mt) REVERT: E 81 GLN cc_start: 0.7242 (tt0) cc_final: 0.6912 (tp-100) REVERT: C 199 ASN cc_start: 0.7526 (m-40) cc_final: 0.7098 (m-40) REVERT: C 339 ASP cc_start: 0.8186 (m-30) cc_final: 0.7825 (p0) REVERT: C 443 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7837 (mt) REVERT: F 81 GLN cc_start: 0.7237 (tt0) cc_final: 0.6914 (tp-100) REVERT: D 199 ASN cc_start: 0.7528 (m-40) cc_final: 0.7102 (m-40) REVERT: D 339 ASP cc_start: 0.8186 (m-30) cc_final: 0.7826 (p0) REVERT: D 443 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7841 (mt) REVERT: G 81 GLN cc_start: 0.7252 (tt0) cc_final: 0.6923 (tp-100) outliers start: 58 outliers final: 42 residues processed: 277 average time/residue: 0.3904 time to fit residues: 129.4751 Evaluate side-chains 290 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 244 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain H residue 2 MET Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain E residue 2 MET Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain F residue 2 MET Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 187 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 13 optimal weight: 0.0040 chunk 135 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.149191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.120287 restraints weight = 22901.054| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.66 r_work: 0.3269 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20424 Z= 0.161 Angle : 0.640 13.438 27792 Z= 0.318 Chirality : 0.051 0.551 3096 Planarity : 0.004 0.046 3468 Dihedral : 7.089 56.454 3604 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.41 % Favored : 95.42 % Rotamer: Outliers : 2.94 % Allowed : 14.09 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.17), residues: 2448 helix: -2.69 (1.04), residues: 24 sheet: -0.29 (0.16), residues: 932 loop : -1.04 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 118 TYR 0.021 0.002 TYR F 58 PHE 0.014 0.002 PHE H 100F TRP 0.021 0.001 TRP G 100D HIS 0.003 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00368 (20336) covalent geometry : angle 0.60046 (27572) SS BOND : bond 0.00246 ( 44) SS BOND : angle 0.92255 ( 88) hydrogen bonds : bond 0.03352 ( 556) hydrogen bonds : angle 6.59816 ( 1500) link_ALPHA1-3 : bond 0.01120 ( 4) link_ALPHA1-3 : angle 2.00437 ( 12) link_ALPHA1-6 : bond 0.00901 ( 4) link_ALPHA1-6 : angle 1.43542 ( 12) link_BETA1-2 : bond 0.00541 ( 4) link_BETA1-2 : angle 1.22096 ( 12) link_BETA1-4 : bond 0.00739 ( 8) link_BETA1-4 : angle 2.34561 ( 24) link_NAG-ASN : bond 0.00605 ( 24) link_NAG-ASN : angle 4.00566 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 249 time to evaluate : 0.809 Fit side-chains REVERT: A 283 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7675 (ttt90) REVERT: A 339 ASP cc_start: 0.8207 (m-30) cc_final: 0.7839 (p0) REVERT: H 81 GLN cc_start: 0.7225 (tt0) cc_final: 0.6887 (tp-100) REVERT: B 283 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7668 (ttt90) REVERT: B 339 ASP cc_start: 0.8225 (m-30) cc_final: 0.7847 (p0) REVERT: E 81 GLN cc_start: 0.7215 (tt0) cc_final: 0.6874 (tp-100) REVERT: C 283 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7677 (ttt90) REVERT: C 339 ASP cc_start: 0.8211 (m-30) cc_final: 0.7831 (p0) REVERT: F 81 GLN cc_start: 0.7210 (tt0) cc_final: 0.6874 (tp-100) REVERT: D 283 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7646 (ttt90) REVERT: D 339 ASP cc_start: 0.8204 (m-30) cc_final: 0.7840 (p0) REVERT: G 81 GLN cc_start: 0.7225 (tt0) cc_final: 0.6884 (tp-100) outliers start: 63 outliers final: 45 residues processed: 289 average time/residue: 0.3963 time to fit residues: 136.5849 Evaluate side-chains 294 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 245 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 337 CYS Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 283 ARG Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 93 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 337 CYS Chi-restraints excluded: chain F residue 39 GLN Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain D residue 151 ASP Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 283 ARG Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain D residue 337 CYS Chi-restraints excluded: chain G residue 39 GLN Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 11 optimal weight: 6.9990 chunk 224 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119822 restraints weight = 23027.662| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.67 r_work: 0.3260 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20424 Z= 0.174 Angle : 0.651 13.791 27792 Z= 0.324 Chirality : 0.052 0.559 3096 Planarity : 0.004 0.046 3468 Dihedral : 7.186 56.395 3604 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.88 % Favored : 95.96 % Rotamer: Outliers : 2.99 % Allowed : 14.09 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.00 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.17), residues: 2448 helix: -2.70 (1.05), residues: 24 sheet: -0.38 (0.16), residues: 952 loop : -1.01 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 118 TYR 0.013 0.002 TYR A 121 PHE 0.015 0.002 PHE H 100F TRP 0.027 0.001 TRP G 100D HIS 0.003 0.001 HIS D 184 Details of bonding type rmsd covalent geometry : bond 0.00398 (20336) covalent geometry : angle 0.61018 (27572) SS BOND : bond 0.00270 ( 44) SS BOND : angle 0.94707 ( 88) hydrogen bonds : bond 0.03395 ( 556) hydrogen bonds : angle 6.64780 ( 1500) link_ALPHA1-3 : bond 0.01093 ( 4) link_ALPHA1-3 : angle 2.11467 ( 12) link_ALPHA1-6 : bond 0.00869 ( 4) link_ALPHA1-6 : angle 1.43883 ( 12) link_BETA1-2 : bond 0.00532 ( 4) link_BETA1-2 : angle 1.26921 ( 12) link_BETA1-4 : bond 0.00721 ( 8) link_BETA1-4 : angle 2.40698 ( 24) link_NAG-ASN : bond 0.00607 ( 24) link_NAG-ASN : angle 4.08664 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5663.02 seconds wall clock time: 97 minutes 59.46 seconds (5879.46 seconds total)