Starting phenix.real_space_refine on Sat Sep 12 16:16:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6dg7_7882/09_2026/6dg7_7882.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dg7_7882/09_2026/6dg7_7882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dg7_7882/09_2026/6dg7_7882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dg7_7882/09_2026/6dg7_7882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dg7_7882/09_2026/6dg7_7882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dg7_7882/09_2026/6dg7_7882.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6dg7_7882/09_2026/6dg7_7882.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6dg7_7882/09_2026/6dg7_7882.cif" } resolution = 3.32 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= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 10980 2.51 5 N 2690 2.21 5 O 3005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16720 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3235 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3235 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3235 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3235 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 3235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3235 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 370} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'SRO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'SRO': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.27, per 1000 atoms: 0.20 Number of scatterers: 16720 At special positions: 0 Unit cell: (104.272, 108.528, 172.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 3005 8.00 N 2690 7.00 C 10980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG F 1 " - " ASN A 82 " " NAG H 1 " - " ASN A 148 " " NAG I 1 " - " ASN B 164 " " NAG J 1 " - " ASN B 82 " " NAG N 1 " - " ASN C 148 " " NAG O 1 " - " ASN D 164 " " NAG P 1 " - " ASN D 82 " " NAG S 1 " - " ASN E 82 " " NAG T 1 " - " ASN E 148 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 519.9 milliseconds 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3800 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 43.5% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 3.588A pdb=" N SER A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 221 through 242 removed outlier: 4.103A pdb=" N VAL A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 249 through 271 removed outlier: 4.021A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 removed outlier: 3.959A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 332 removed outlier: 3.518A pdb=" N LEU A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 462 removed outlier: 3.993A pdb=" N LEU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 20 removed outlier: 3.587A pdb=" N SER B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 176 Processing helix chain 'B' and resid 221 through 242 removed outlier: 4.103A pdb=" N VAL B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 249 through 271 removed outlier: 4.022A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 308 removed outlier: 3.957A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 332 removed outlier: 3.519A pdb=" N LEU B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 325 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 462 removed outlier: 3.993A pdb=" N LEU B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 20 removed outlier: 3.588A pdb=" N SER C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 221 through 242 removed outlier: 4.103A pdb=" N VAL C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 249 through 271 removed outlier: 4.022A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP C 271 " --> pdb=" O ILE C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 308 removed outlier: 3.957A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 332 removed outlier: 3.518A pdb=" N LEU C 321 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 325 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 462 removed outlier: 3.993A pdb=" N LEU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.587A pdb=" N SER D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 176 Processing helix chain 'D' and resid 221 through 242 removed outlier: 4.103A pdb=" N VAL D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 249 through 271 removed outlier: 4.022A pdb=" N SER D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 308 removed outlier: 3.957A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 332 removed outlier: 3.518A pdb=" N LEU D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 325 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE D 329 " --> pdb=" O VAL D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 462 removed outlier: 3.994A pdb=" N LEU D 402 " --> pdb=" O ALA D 398 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 20 removed outlier: 3.588A pdb=" N SER E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 176 Processing helix chain 'E' and resid 221 through 242 removed outlier: 4.104A pdb=" N VAL E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 249 through 271 removed outlier: 4.020A pdb=" N SER E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP E 271 " --> pdb=" O ILE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 removed outlier: 3.958A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 332 removed outlier: 3.517A pdb=" N LEU E 321 " --> pdb=" O VAL E 317 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL E 325 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU E 326 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE E 329 " --> pdb=" O VAL E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 462 removed outlier: 3.993A pdb=" N LEU E 402 " --> pdb=" O ALA E 398 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU E 403 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 134 removed outlier: 3.521A pdb=" N TYR A 64 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 129 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE A 62 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN A 50 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N TRP A 63 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR A 46 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ARG A 65 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE A 44 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N TYR A 67 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ASP A 42 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N THR A 69 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N SER A 40 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 166 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 88 removed outlier: 3.569A pdb=" N ILE A 88 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 148 through 154 Processing sheet with id=AA4, first strand: chain 'A' and resid 148 through 154 removed outlier: 3.735A pdb=" N GLU A 209 " --> pdb=" O LYS A 197 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 122 through 134 removed outlier: 3.522A pdb=" N TYR B 64 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU B 129 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE B 62 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN B 50 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N TYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ASP B 42 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N THR B 69 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N SER B 40 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 166 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.568A pdb=" N ILE B 88 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 148 through 154 Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 154 removed outlier: 3.734A pdb=" N GLU B 209 " --> pdb=" O LYS B 197 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 122 through 134 removed outlier: 3.521A pdb=" N TYR C 64 " --> pdb=" O LYS C 127 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU C 129 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE C 62 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN C 50 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N TRP C 63 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR C 46 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ARG C 65 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE C 44 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N TYR C 67 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ASP C 42 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N THR C 69 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 9.314A pdb=" N SER C 40 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR C 166 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 87 through 88 removed outlier: 3.568A pdb=" N ILE C 88 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 148 through 154 Processing sheet with id=AB3, first strand: chain 'C' and resid 148 through 154 removed outlier: 3.735A pdb=" N GLU C 209 " --> pdb=" O LYS C 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 122 through 134 removed outlier: 3.521A pdb=" N TYR D 64 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU D 129 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE D 62 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN D 50 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ARG D 65 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE D 44 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N TYR D 67 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ASP D 42 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N THR D 69 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N SER D 40 " --> pdb=" O THR D 69 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR D 166 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 87 through 88 removed outlier: 3.568A pdb=" N ILE D 88 " --> pdb=" O VAL D 115 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 148 through 154 Processing sheet with id=AB7, first strand: chain 'D' and resid 148 through 154 removed outlier: 3.734A pdb=" N GLU D 209 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 122 through 134 removed outlier: 3.522A pdb=" N TYR E 64 " --> pdb=" O LYS E 127 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU E 129 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE E 62 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASN E 50 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ARG E 65 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE E 44 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N TYR E 67 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ASP E 42 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N THR E 69 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N SER E 40 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR E 166 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 87 through 88 removed outlier: 3.568A pdb=" N ILE E 88 " --> pdb=" O VAL E 115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 148 through 154 Processing sheet with id=AC2, first strand: chain 'E' and resid 148 through 154 removed outlier: 3.735A pdb=" N GLU E 209 " --> pdb=" O LYS E 197 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2415 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: 2.44 Time building geometry restraints manager: 1.53 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: 4903 1.34 - 1.46: 3356 1.46 - 1.58: 8839 1.58 - 1.69: 2 1.69 - 1.81: 70 Bond restraints: 17170 Sorted by residual: bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.511 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.597 -0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.473 -0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 17165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 22557 2.41 - 4.82: 660 4.82 - 7.23: 179 7.23 - 9.64: 49 9.64 - 12.05: 5 Bond angle restraints: 23450 Sorted by residual: angle pdb=" C GLU B 78 " pdb=" N ASP B 79 " pdb=" CA ASP B 79 " ideal model delta sigma weight residual 121.54 133.59 -12.05 1.91e+00 2.74e-01 3.98e+01 angle pdb=" C GLU E 78 " pdb=" N ASP E 79 " pdb=" CA ASP E 79 " ideal model delta sigma weight residual 121.54 133.55 -12.01 1.91e+00 2.74e-01 3.95e+01 angle pdb=" C GLU D 78 " pdb=" N ASP D 79 " pdb=" CA ASP D 79 " ideal model delta sigma weight residual 121.54 133.55 -12.01 1.91e+00 2.74e-01 3.95e+01 angle pdb=" C GLU C 78 " pdb=" N ASP C 79 " pdb=" CA ASP C 79 " ideal model delta sigma weight residual 121.54 133.51 -11.97 1.91e+00 2.74e-01 3.93e+01 angle pdb=" C GLU A 78 " pdb=" N ASP A 79 " pdb=" CA ASP A 79 " ideal model delta sigma weight residual 121.54 133.51 -11.97 1.91e+00 2.74e-01 3.92e+01 ... (remaining 23445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 9035 15.14 - 30.28: 556 30.28 - 45.42: 191 45.42 - 60.56: 19 60.56 - 75.70: 19 Dihedral angle restraints: 9820 sinusoidal: 3985 harmonic: 5835 Sorted by residual: dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual -86.00 -123.24 37.24 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CB CYS B 135 " pdb=" SG CYS B 135 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual -86.00 -123.24 37.24 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CB CYS D 135 " pdb=" SG CYS D 135 " pdb=" SG CYS D 149 " pdb=" CB CYS D 149 " ideal model delta sinusoidal sigma weight residual -86.00 -123.24 37.24 1 1.00e+01 1.00e-02 1.96e+01 ... (remaining 9817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2398 0.083 - 0.166: 351 0.166 - 0.249: 31 0.249 - 0.332: 7 0.332 - 0.414: 2 Chirality restraints: 2789 Sorted by residual: chirality pdb=" C2 NAG I 1 " pdb=" C1 NAG I 1 " pdb=" C3 NAG I 1 " pdb=" N2 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.08 -0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN D 82 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C4 NAG R 1 " pdb=" C3 NAG R 1 " pdb=" C5 NAG R 1 " pdb=" O4 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.20 -0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 2786 not shown) Planarity restraints: 2839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 219 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO A 220 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 219 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO C 220 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 220 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 220 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 219 " 0.034 5.00e-02 4.00e+02 5.25e-02 4.42e+00 pdb=" N PRO E 220 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 220 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 220 " 0.029 5.00e-02 4.00e+02 ... (remaining 2836 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4654 2.82 - 3.34: 15112 3.34 - 3.86: 26856 3.86 - 4.38: 27703 4.38 - 4.90: 48708 Nonbonded interactions: 123033 Sorted by model distance: nonbonded pdb=" ND2 ASN B 50 " pdb=" OD1 ASN C 55 " model vdw 2.303 3.120 nonbonded pdb=" O ASN A 50 " pdb=" OG1 THR A 59 " model vdw 2.319 3.040 nonbonded pdb=" O ASN E 50 " pdb=" OG1 THR E 59 " model vdw 2.319 3.040 nonbonded pdb=" O ASN B 50 " pdb=" OG1 THR B 59 " model vdw 2.319 3.040 nonbonded pdb=" O ASN D 50 " pdb=" OG1 THR D 59 " model vdw 2.320 3.040 ... (remaining 123028 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 462) selection = (chain 'B' and resid 8 through 462) selection = (chain 'C' and resid 8 through 462) selection = chain 'D' selection = (chain 'E' and resid 8 through 462) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' } 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: 1.600 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.440 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 0.105 17204 Z= 0.302 Angle : 1.145 17.456 23547 Z= 0.560 Chirality : 0.058 0.414 2789 Planarity : 0.007 0.053 2830 Dihedral : 11.641 75.699 6005 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.27 % Allowed : 8.56 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.84 (0.16), residues: 1935 helix: -1.12 (0.15), residues: 790 sheet: -1.57 (0.20), residues: 440 loop : -2.84 (0.18), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 322 TYR 0.017 0.002 TYR E 286 PHE 0.028 0.003 PHE C 412 TRP 0.014 0.002 TRP E 94 HIS 0.002 0.000 HIS C 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.30 (17170) covalent geometry : angle 1.10462 / 0.55 (23450) SS BOND : bond 0.00075 / 0.04 ( 5) SS BOND : angle 0.46396 / 0.26 ( 10) hydrogen bonds : bond 0.16934 / 11.42 ( 790) hydrogen bonds : angle 6.99825 / 4.81 ( 2415) link_BETA1-4 : bond 0.01139 / 0.84 ( 20) link_BETA1-4 : angle 2.68639 / 1.72 ( 60) link_NAG-ASN : bond 0.03162 / 1.90 ( 9) link_NAG-ASN : angle 8.19819 / 5.53 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 320 TRP cc_start: 0.7124 (m100) cc_final: 0.6500 (m100) REVERT: A 433 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8109 (tt) REVERT: B 30 VAL cc_start: 0.8779 (m) cc_final: 0.8566 (m) REVERT: B 210 MET cc_start: 0.8513 (tpp) cc_final: 0.8301 (tpt) REVERT: B 320 TRP cc_start: 0.7307 (m100) cc_final: 0.6700 (m100) REVERT: C 320 TRP cc_start: 0.7394 (m100) cc_final: 0.6575 (m100) REVERT: D 320 TRP cc_start: 0.7302 (m100) cc_final: 0.6451 (m100) REVERT: E 320 TRP cc_start: 0.7164 (m100) cc_final: 0.6623 (m100) REVERT: E 419 MET cc_start: 0.9039 (mmm) cc_final: 0.8419 (mmm) outliers start: 23 outliers final: 0 residues processed: 181 average time/residue: 0.1139 time to fit residues: 32.6453 Evaluate side-chains 69 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 164 ASN A 309 HIS A 404 GLN B 130 GLN B 147 GLN B 309 HIS C 130 GLN C 164 ASN C 404 GLN D 130 GLN D 309 HIS D 404 GLN E 130 GLN ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS E 404 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.076048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.060348 restraints weight = 66170.619| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 4.02 r_work: 0.3151 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17204 Z= 0.134 Angle : 0.678 11.968 23547 Z= 0.322 Chirality : 0.043 0.343 2789 Planarity : 0.005 0.029 2830 Dihedral : 5.735 62.446 2172 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.87 % Allowed : 12.71 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.55 (0.19), residues: 1935 helix: 1.45 (0.18), residues: 790 sheet: -0.71 (0.23), residues: 390 loop : -2.19 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 315 TYR 0.017 0.001 TYR B 223 PHE 0.017 0.002 PHE B 265 TRP 0.020 0.002 TRP E 331 HIS 0.002 0.000 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (17170) covalent geometry : angle 0.64346 / 0.31 (23450) SS BOND : bond 0.00291 / 0.16 ( 5) SS BOND : angle 0.36002 / 0.21 ( 10) hydrogen bonds : bond 0.05249 / 3.48 ( 790) hydrogen bonds : angle 4.68765 / 3.18 ( 2415) link_BETA1-4 : bond 0.00384 / 0.23 ( 20) link_BETA1-4 : angle 1.64614 / 1.05 ( 60) link_NAG-ASN : bond 0.01288 / 0.85 ( 9) link_NAG-ASN : angle 5.98365 / 4.17 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 81 time to evaluate : 0.465 Fit side-chains REVERT: A 320 TRP cc_start: 0.7680 (m100) cc_final: 0.6901 (m100) REVERT: A 419 MET cc_start: 0.9178 (tmm) cc_final: 0.8951 (tmm) REVERT: B 320 TRP cc_start: 0.8049 (m100) cc_final: 0.7180 (m100) REVERT: C 210 MET cc_start: 0.8855 (tpp) cc_final: 0.8403 (tpt) REVERT: C 320 TRP cc_start: 0.7864 (m100) cc_final: 0.6995 (m100) REVERT: D 221 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6852 (tt) REVERT: D 419 MET cc_start: 0.9061 (tmm) cc_final: 0.8836 (tmm) REVERT: E 221 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7106 (tt) REVERT: E 320 TRP cc_start: 0.7893 (m100) cc_final: 0.7116 (m100) REVERT: E 419 MET cc_start: 0.9163 (mmm) cc_final: 0.8586 (mmm) outliers start: 70 outliers final: 23 residues processed: 142 average time/residue: 0.1186 time to fit residues: 26.2459 Evaluate side-chains 92 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 116 TYR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 445 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 37 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 158 HIS B 158 HIS C 158 HIS D 158 HIS E 158 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.065187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.046286 restraints weight = 67451.583| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 4.07 r_work: 0.2744 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 17204 Z= 0.341 Angle : 0.916 11.389 23547 Z= 0.450 Chirality : 0.050 0.487 2789 Planarity : 0.005 0.032 2830 Dihedral : 5.760 41.399 2170 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.64 % Allowed : 14.31 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.03 (0.19), residues: 1935 helix: 2.00 (0.17), residues: 795 sheet: -0.86 (0.23), residues: 415 loop : -1.73 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 315 TYR 0.027 0.003 TYR B 286 PHE 0.015 0.002 PHE A 181 TRP 0.034 0.003 TRP A 168 HIS 0.005 0.001 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.34 (17170) covalent geometry : angle 0.89013 / 0.44 (23450) SS BOND : bond 0.00467 / 0.25 ( 5) SS BOND : angle 1.11143 / 0.65 ( 10) hydrogen bonds : bond 0.06488 / 4.23 ( 790) hydrogen bonds : angle 4.56985 / 3.11 ( 2415) link_BETA1-4 : bond 0.00648 / 0.48 ( 20) link_BETA1-4 : angle 1.91802 / 1.19 ( 60) link_NAG-ASN : bond 0.01337 / 0.94 ( 9) link_NAG-ASN : angle 5.85546 / 4.13 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 71 time to evaluate : 0.677 Fit side-chains REVERT: A 210 MET cc_start: 0.9091 (tpp) cc_final: 0.8882 (tpp) REVERT: A 320 TRP cc_start: 0.7965 (m100) cc_final: 0.7102 (m100) REVERT: A 419 MET cc_start: 0.9282 (tmm) cc_final: 0.9058 (tmm) REVERT: B 320 TRP cc_start: 0.8242 (m100) cc_final: 0.7351 (m100) REVERT: C 210 MET cc_start: 0.8980 (tpp) cc_final: 0.8633 (tpp) REVERT: C 320 TRP cc_start: 0.7988 (m100) cc_final: 0.7071 (m100) REVERT: C 416 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8890 (tpp80) REVERT: C 419 MET cc_start: 0.9398 (tmm) cc_final: 0.9069 (tmm) REVERT: D 419 MET cc_start: 0.9262 (tmm) cc_final: 0.9036 (tmm) REVERT: E 286 TYR cc_start: 0.8229 (OUTLIER) cc_final: 0.7959 (t80) REVERT: E 320 TRP cc_start: 0.8120 (m100) cc_final: 0.7496 (m100) outliers start: 84 outliers final: 35 residues processed: 143 average time/residue: 0.1167 time to fit residues: 26.3054 Evaluate side-chains 96 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 59 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 416 ARG Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 286 TYR Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 24 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 173 optimal weight: 0.0060 chunk 116 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.067166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.048553 restraints weight = 66262.121| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 4.08 r_work: 0.2806 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17204 Z= 0.138 Angle : 0.693 11.922 23547 Z= 0.323 Chirality : 0.044 0.397 2789 Planarity : 0.003 0.030 2830 Dihedral : 4.995 37.390 2170 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.59 % Allowed : 16.85 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.54 (0.19), residues: 1935 helix: 2.62 (0.18), residues: 795 sheet: -0.58 (0.23), residues: 380 loop : -1.69 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 218 TYR 0.027 0.002 TYR B 223 PHE 0.010 0.001 PHE A 181 TRP 0.018 0.001 TRP B 156 HIS 0.001 0.000 HIS E 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (17170) covalent geometry : angle 0.66553 / 0.32 (23450) SS BOND : bond 0.00185 / 0.10 ( 5) SS BOND : angle 0.55976 / 0.33 ( 10) hydrogen bonds : bond 0.05346 / 3.53 ( 790) hydrogen bonds : angle 3.97333 / 2.71 ( 2415) link_BETA1-4 : bond 0.00471 / 0.30 ( 20) link_BETA1-4 : angle 1.38093 / 0.87 ( 60) link_NAG-ASN : bond 0.01195 / 0.81 ( 9) link_NAG-ASN : angle 5.42825 / 3.88 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 64 time to evaluate : 0.639 Fit side-chains REVERT: A 116 TYR cc_start: 0.9026 (OUTLIER) cc_final: 0.8630 (m-80) REVERT: A 320 TRP cc_start: 0.7944 (m100) cc_final: 0.7083 (m100) REVERT: A 419 MET cc_start: 0.9244 (tmm) cc_final: 0.9015 (tmm) REVERT: B 210 MET cc_start: 0.9131 (tpp) cc_final: 0.8514 (tpt) REVERT: B 320 TRP cc_start: 0.8241 (m100) cc_final: 0.7344 (m100) REVERT: C 320 TRP cc_start: 0.8028 (m100) cc_final: 0.7124 (m100) REVERT: C 416 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8800 (tpp-160) REVERT: D 419 MET cc_start: 0.9242 (tmm) cc_final: 0.9011 (tmm) REVERT: E 320 TRP cc_start: 0.8105 (m100) cc_final: 0.7457 (m100) outliers start: 65 outliers final: 38 residues processed: 125 average time/residue: 0.0975 time to fit residues: 20.9053 Evaluate side-chains 95 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 55 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 416 ARG Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 323 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 144 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.066427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.047848 restraints weight = 66631.294| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 4.11 r_work: 0.2779 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17204 Z= 0.164 Angle : 0.674 11.826 23547 Z= 0.314 Chirality : 0.043 0.359 2789 Planarity : 0.003 0.026 2830 Dihedral : 4.666 27.494 2170 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.64 % Allowed : 16.41 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.74 (0.20), residues: 1935 helix: 2.83 (0.18), residues: 795 sheet: -0.43 (0.26), residues: 315 loop : -1.58 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 218 TYR 0.020 0.002 TYR E 448 PHE 0.012 0.001 PHE C 144 TRP 0.024 0.001 TRP A 187 HIS 0.002 0.000 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (17170) covalent geometry : angle 0.64732 / 0.31 (23450) SS BOND : bond 0.00129 / 0.07 ( 5) SS BOND : angle 0.59712 / 0.34 ( 10) hydrogen bonds : bond 0.05156 / 3.39 ( 790) hydrogen bonds : angle 3.90999 / 2.67 ( 2415) link_BETA1-4 : bond 0.00368 / 0.23 ( 20) link_BETA1-4 : angle 1.39964 / 0.89 ( 60) link_NAG-ASN : bond 0.01031 / 0.73 ( 9) link_NAG-ASN : angle 5.25746 / 3.78 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 54 time to evaluate : 0.536 Fit side-chains REVERT: A 116 TYR cc_start: 0.9046 (OUTLIER) cc_final: 0.8631 (m-80) REVERT: A 320 TRP cc_start: 0.7943 (m100) cc_final: 0.7130 (m100) REVERT: A 419 MET cc_start: 0.9337 (tmm) cc_final: 0.9083 (tmm) REVERT: A 443 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8031 (tt) REVERT: B 129 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9426 (pp) REVERT: B 210 MET cc_start: 0.9132 (tpp) cc_final: 0.8593 (tpt) REVERT: B 320 TRP cc_start: 0.8251 (m100) cc_final: 0.7354 (m100) REVERT: C 320 TRP cc_start: 0.8077 (m100) cc_final: 0.7182 (m100) REVERT: C 443 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8022 (tt) REVERT: D 419 MET cc_start: 0.9277 (tmm) cc_final: 0.9048 (tmm) REVERT: D 443 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7992 (tt) REVERT: E 210 MET cc_start: 0.9180 (tpp) cc_final: 0.8780 (tpt) REVERT: E 320 TRP cc_start: 0.8130 (m100) cc_final: 0.7463 (m100) REVERT: E 443 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7911 (tt) outliers start: 84 outliers final: 52 residues processed: 137 average time/residue: 0.0908 time to fit residues: 21.5129 Evaluate side-chains 109 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 51 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 116 TYR Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 445 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 91 optimal weight: 0.3980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.047324 restraints weight = 65851.345| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 4.11 r_work: 0.2770 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17204 Z= 0.161 Angle : 0.677 12.255 23547 Z= 0.312 Chirality : 0.043 0.346 2789 Planarity : 0.003 0.027 2830 Dihedral : 4.530 23.575 2170 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.92 % Allowed : 16.13 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.77 (0.20), residues: 1935 helix: 2.94 (0.18), residues: 790 sheet: -0.48 (0.26), residues: 315 loop : -1.61 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 218 TYR 0.032 0.002 TYR B 223 PHE 0.013 0.001 PHE C 144 TRP 0.019 0.001 TRP B 168 HIS 0.002 0.000 HIS C 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (17170) covalent geometry : angle 0.65118 / 0.31 (23450) SS BOND : bond 0.00135 / 0.08 ( 5) SS BOND : angle 0.65625 / 0.37 ( 10) hydrogen bonds : bond 0.05036 / 3.30 ( 790) hydrogen bonds : angle 3.82906 / 2.61 ( 2415) link_BETA1-4 : bond 0.00311 / 0.20 ( 20) link_BETA1-4 : angle 1.34175 / 0.86 ( 60) link_NAG-ASN : bond 0.00976 / 0.69 ( 9) link_NAG-ASN : angle 5.17452 / 3.71 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 50 time to evaluate : 0.671 Fit side-chains REVERT: A 320 TRP cc_start: 0.8034 (m100) cc_final: 0.7202 (m100) REVERT: A 419 MET cc_start: 0.9333 (tmm) cc_final: 0.9109 (ppp) REVERT: A 443 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8032 (tt) REVERT: B 129 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9414 (pp) REVERT: B 210 MET cc_start: 0.9137 (tpp) cc_final: 0.8552 (tpt) REVERT: B 320 TRP cc_start: 0.8274 (m100) cc_final: 0.7379 (m100) REVERT: C 129 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9436 (pp) REVERT: C 320 TRP cc_start: 0.8143 (m100) cc_final: 0.7236 (m100) REVERT: C 443 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8088 (tt) REVERT: D 419 MET cc_start: 0.9271 (tmm) cc_final: 0.9052 (tmm) REVERT: E 210 MET cc_start: 0.9154 (tpp) cc_final: 0.8654 (tpt) REVERT: E 320 TRP cc_start: 0.8222 (m100) cc_final: 0.7555 (m100) REVERT: E 443 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7914 (tt) outliers start: 89 outliers final: 60 residues processed: 138 average time/residue: 0.1018 time to fit residues: 24.3039 Evaluate side-chains 115 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 50 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 442 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 120 optimal weight: 0.9990 chunk 179 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.065347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.046720 restraints weight = 67749.203| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 4.08 r_work: 0.2763 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17204 Z= 0.177 Angle : 0.680 11.712 23547 Z= 0.314 Chirality : 0.042 0.339 2789 Planarity : 0.003 0.028 2830 Dihedral : 4.516 22.017 2170 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.64 % Allowed : 16.80 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.85 (0.20), residues: 1935 helix: 3.01 (0.18), residues: 790 sheet: -0.59 (0.24), residues: 380 loop : -1.56 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 315 TYR 0.020 0.002 TYR E 286 PHE 0.014 0.001 PHE C 144 TRP 0.020 0.001 TRP D 168 HIS 0.002 0.000 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (17170) covalent geometry : angle 0.65510 / 0.31 (23450) SS BOND : bond 0.00125 / 0.07 ( 5) SS BOND : angle 0.68121 / 0.38 ( 10) hydrogen bonds : bond 0.05022 / 3.29 ( 790) hydrogen bonds : angle 3.83001 / 2.62 ( 2415) link_BETA1-4 : bond 0.00310 / 0.21 ( 20) link_BETA1-4 : angle 1.37602 / 0.88 ( 60) link_NAG-ASN : bond 0.00932 / 0.67 ( 9) link_NAG-ASN : angle 5.15531 / 3.70 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 50 time to evaluate : 0.672 Fit side-chains REVERT: A 320 TRP cc_start: 0.8003 (m100) cc_final: 0.7757 (m-90) REVERT: A 419 MET cc_start: 0.9362 (tmm) cc_final: 0.9139 (ppp) REVERT: A 443 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8110 (tt) REVERT: B 129 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9480 (pp) REVERT: B 151 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8818 (pp) REVERT: B 210 MET cc_start: 0.9223 (tpp) cc_final: 0.8630 (tpt) REVERT: B 291 MET cc_start: 0.8722 (tpp) cc_final: 0.8474 (tpp) REVERT: B 320 TRP cc_start: 0.8277 (m100) cc_final: 0.7353 (m100) REVERT: C 129 LEU cc_start: 0.9693 (OUTLIER) cc_final: 0.9483 (pp) REVERT: C 320 TRP cc_start: 0.8096 (m100) cc_final: 0.7189 (m100) REVERT: C 443 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8147 (tt) REVERT: D 419 MET cc_start: 0.9315 (tmm) cc_final: 0.9086 (tmm) REVERT: E 151 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8962 (pp) REVERT: E 210 MET cc_start: 0.9301 (tpp) cc_final: 0.8829 (tpt) REVERT: E 320 TRP cc_start: 0.8203 (m100) cc_final: 0.7539 (m100) REVERT: E 443 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8011 (tt) outliers start: 84 outliers final: 63 residues processed: 133 average time/residue: 0.0953 time to fit residues: 22.3802 Evaluate side-chains 117 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 47 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 108 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.065930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.047343 restraints weight = 67326.731| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.09 r_work: 0.2780 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17204 Z= 0.140 Angle : 0.666 11.705 23547 Z= 0.304 Chirality : 0.042 0.319 2789 Planarity : 0.003 0.029 2830 Dihedral : 4.358 20.458 2170 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.20 % Allowed : 17.35 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.92 (0.20), residues: 1935 helix: 3.11 (0.18), residues: 790 sheet: -0.50 (0.26), residues: 315 loop : -1.53 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 315 TYR 0.032 0.002 TYR B 223 PHE 0.014 0.001 PHE C 144 TRP 0.016 0.001 TRP D 168 HIS 0.002 0.000 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (17170) covalent geometry : angle 0.64147 / 0.30 (23450) SS BOND : bond 0.00118 / 0.06 ( 5) SS BOND : angle 0.57917 / 0.33 ( 10) hydrogen bonds : bond 0.04808 / 3.16 ( 790) hydrogen bonds : angle 3.69777 / 2.53 ( 2415) link_BETA1-4 : bond 0.00347 / 0.24 ( 20) link_BETA1-4 : angle 1.33262 / 0.85 ( 60) link_NAG-ASN : bond 0.00982 / 0.69 ( 9) link_NAG-ASN : angle 5.07386 / 3.65 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 53 time to evaluate : 0.630 Fit side-chains REVERT: A 320 TRP cc_start: 0.8008 (m100) cc_final: 0.7753 (m-90) REVERT: A 419 MET cc_start: 0.9360 (tmm) cc_final: 0.9138 (ppp) REVERT: A 443 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8035 (tt) REVERT: B 151 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8727 (pp) REVERT: B 210 MET cc_start: 0.9212 (tpp) cc_final: 0.8639 (tpt) REVERT: B 320 TRP cc_start: 0.8299 (m100) cc_final: 0.7377 (m100) REVERT: C 221 LEU cc_start: 0.8003 (tm) cc_final: 0.7788 (mm) REVERT: C 320 TRP cc_start: 0.8084 (m100) cc_final: 0.7178 (m100) REVERT: C 443 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8150 (tt) REVERT: D 419 MET cc_start: 0.9301 (tmm) cc_final: 0.9067 (tmm) REVERT: E 143 PRO cc_start: 0.8942 (Cg_exo) cc_final: 0.8732 (Cg_endo) REVERT: E 210 MET cc_start: 0.9261 (tpp) cc_final: 0.8769 (tpt) REVERT: E 320 TRP cc_start: 0.8206 (m100) cc_final: 0.7543 (m100) REVERT: E 443 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8008 (tt) outliers start: 76 outliers final: 59 residues processed: 128 average time/residue: 0.1061 time to fit residues: 23.0554 Evaluate side-chains 112 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 49 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 161 optimal weight: 5.9990 chunk 123 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 27 optimal weight: 0.0980 chunk 21 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.064942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.046279 restraints weight = 67473.074| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 4.06 r_work: 0.2749 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17204 Z= 0.181 Angle : 0.701 14.622 23547 Z= 0.320 Chirality : 0.042 0.339 2789 Planarity : 0.003 0.030 2830 Dihedral : 4.430 19.288 2170 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.09 % Allowed : 17.68 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.90 (0.20), residues: 1935 helix: 3.10 (0.18), residues: 790 sheet: -0.65 (0.26), residues: 320 loop : -1.48 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 315 TYR 0.022 0.002 TYR E 286 PHE 0.014 0.001 PHE C 144 TRP 0.022 0.001 TRP B 168 HIS 0.002 0.000 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (17170) covalent geometry : angle 0.67646 / 0.31 (23450) SS BOND : bond 0.00123 / 0.07 ( 5) SS BOND : angle 0.73942 / 0.41 ( 10) hydrogen bonds : bond 0.04940 / 3.23 ( 790) hydrogen bonds : angle 3.79723 / 2.59 ( 2415) link_BETA1-4 : bond 0.00306 / 0.21 ( 20) link_BETA1-4 : angle 1.40079 / 0.90 ( 60) link_NAG-ASN : bond 0.00914 / 0.66 ( 9) link_NAG-ASN : angle 5.10551 / 3.66 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 49 time to evaluate : 0.602 Fit side-chains REVERT: A 291 MET cc_start: 0.8289 (tpp) cc_final: 0.7334 (tpp) REVERT: A 320 TRP cc_start: 0.8090 (m100) cc_final: 0.7550 (m-10) REVERT: A 419 MET cc_start: 0.9362 (tmm) cc_final: 0.9146 (ppp) REVERT: A 443 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8156 (tt) REVERT: B 151 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8731 (pp) REVERT: B 210 MET cc_start: 0.9238 (tpp) cc_final: 0.8673 (tpt) REVERT: B 320 TRP cc_start: 0.8301 (m100) cc_final: 0.7549 (m-10) REVERT: C 320 TRP cc_start: 0.8108 (m100) cc_final: 0.7479 (m-90) REVERT: C 443 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8053 (tt) REVERT: D 419 MET cc_start: 0.9325 (tmm) cc_final: 0.9086 (tmm) REVERT: E 210 MET cc_start: 0.9293 (tpp) cc_final: 0.8810 (tpt) REVERT: E 320 TRP cc_start: 0.8245 (m100) cc_final: 0.7390 (m100) outliers start: 74 outliers final: 61 residues processed: 121 average time/residue: 0.0991 time to fit residues: 20.8236 Evaluate side-chains 112 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 48 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 18 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.065075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.046479 restraints weight = 66826.629| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 4.03 r_work: 0.2751 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17204 Z= 0.164 Angle : 0.698 11.870 23547 Z= 0.317 Chirality : 0.042 0.325 2789 Planarity : 0.003 0.030 2830 Dihedral : 4.417 19.616 2170 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.70 % Allowed : 18.34 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.90 (0.20), residues: 1935 helix: 3.12 (0.18), residues: 790 sheet: -0.67 (0.26), residues: 320 loop : -1.51 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 315 TYR 0.026 0.002 TYR B 223 PHE 0.013 0.001 PHE C 144 TRP 0.019 0.001 TRP B 168 HIS 0.002 0.000 HIS B 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (17170) covalent geometry : angle 0.67444 / 0.31 (23450) SS BOND : bond 0.00102 / 0.06 ( 5) SS BOND : angle 0.66160 / 0.37 ( 10) hydrogen bonds : bond 0.04883 / 3.20 ( 790) hydrogen bonds : angle 3.74228 / 2.56 ( 2415) link_BETA1-4 : bond 0.00319 / 0.22 ( 20) link_BETA1-4 : angle 1.35839 / 0.87 ( 60) link_NAG-ASN : bond 0.00923 / 0.65 ( 9) link_NAG-ASN : angle 5.06119 / 3.64 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 49 time to evaluate : 0.664 Fit side-chains REVERT: A 291 MET cc_start: 0.8583 (tpp) cc_final: 0.7669 (tpp) REVERT: A 320 TRP cc_start: 0.8102 (m100) cc_final: 0.7548 (m-10) REVERT: A 419 MET cc_start: 0.9422 (tmm) cc_final: 0.9219 (ppp) REVERT: A 443 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8084 (tt) REVERT: B 151 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8722 (pp) REVERT: B 210 MET cc_start: 0.9226 (tpp) cc_final: 0.8658 (tpt) REVERT: B 320 TRP cc_start: 0.8312 (m100) cc_final: 0.7536 (m-10) REVERT: C 291 MET cc_start: 0.8616 (tpp) cc_final: 0.7893 (tpp) REVERT: C 320 TRP cc_start: 0.8123 (m100) cc_final: 0.7434 (m-90) REVERT: C 443 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8092 (tt) REVERT: D 419 MET cc_start: 0.9367 (tmm) cc_final: 0.9111 (tmm) REVERT: E 210 MET cc_start: 0.9292 (tpp) cc_final: 0.8823 (tpt) REVERT: E 320 TRP cc_start: 0.8259 (m100) cc_final: 0.7398 (m100) outliers start: 67 outliers final: 62 residues processed: 115 average time/residue: 0.1029 time to fit residues: 20.5198 Evaluate side-chains 112 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 47 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 132 VAL Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 295 VAL Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 125 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 147 optimal weight: 0.0010 chunk 29 optimal weight: 0.9990 chunk 164 optimal weight: 0.0010 chunk 168 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 187 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.066341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.047902 restraints weight = 66666.655| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 4.02 r_work: 0.2799 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17204 Z= 0.120 Angle : 0.676 12.047 23547 Z= 0.304 Chirality : 0.042 0.297 2789 Planarity : 0.003 0.029 2830 Dihedral : 4.156 17.403 2170 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.15 % Allowed : 19.06 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.99 (0.20), residues: 1935 helix: 3.10 (0.18), residues: 800 sheet: -0.52 (0.26), residues: 320 loop : -1.46 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 315 TYR 0.025 0.001 TYR E 262 PHE 0.013 0.001 PHE C 144 TRP 0.013 0.001 TRP C 156 HIS 0.001 0.000 HIS E 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (17170) covalent geometry : angle 0.65289 / 0.30 (23450) SS BOND : bond 0.00063 / 0.04 ( 5) SS BOND : angle 0.42855 / 0.24 ( 10) hydrogen bonds : bond 0.04515 / 2.96 ( 790) hydrogen bonds : angle 3.54173 / 2.42 ( 2415) link_BETA1-4 : bond 0.00390 / 0.27 ( 20) link_BETA1-4 : angle 1.30964 / 0.84 ( 60) link_NAG-ASN : bond 0.01042 / 0.73 ( 9) link_NAG-ASN : angle 4.94382 / 3.57 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3431.25 seconds wall clock time: 59 minutes 41.11 seconds (3581.11 seconds total)