Starting phenix.real_space_refine on Tue Nov 18 20:01:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dg7_7882/11_2025/6dg7_7882.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dg7_7882/11_2025/6dg7_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_7882/11_2025/6dg7_7882.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dg7_7882/11_2025/6dg7_7882.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dg7_7882/11_2025/6dg7_7882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dg7_7882/11_2025/6dg7_7882.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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: 4.31, per 1000 atoms: 0.26 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: 1.66 Conformation dependent library (CDL) restraints added in 657.1 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: 0.65 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: 2.69 Time building geometry restraints manager: 2.15 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 - 23.77: 10005 23.77 - 47.54: 440 47.54 - 71.31: 43 71.31 - 95.08: 34 95.08 - 118.85: 23 Dihedral angle restraints: 10545 sinusoidal: 4710 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 10542 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.430 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 : 14.309 118.851 6730 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 covalent geometry : bond 0.00547 (17170) covalent geometry : angle 1.10462 (23450) SS BOND : bond 0.00075 ( 5) SS BOND : angle 0.46396 ( 10) hydrogen bonds : bond 0.16934 ( 790) hydrogen bonds : angle 6.99825 ( 2415) link_BETA1-4 : bond 0.01139 ( 20) link_BETA1-4 : angle 2.68639 ( 60) link_NAG-ASN : bond 0.03162 ( 9) link_NAG-ASN : angle 8.19819 ( 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 : 0.643 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: 0.8780 (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: 0.1287 time to fit residues: 36.4296 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 : 0.704 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 E 309 HIS E 404 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.076000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.059896 restraints weight = 68190.308| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 4.11 r_work: 0.3141 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17204 Z= 0.140 Angle : 0.703 12.045 23547 Z= 0.329 Chirality : 0.044 0.340 2789 Planarity : 0.005 0.037 2830 Dihedral : 10.704 88.744 2897 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.87 % Allowed : 12.76 % Favored : 83.37 % 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: -0.56 (0.19), residues: 1935 helix: 1.41 (0.18), residues: 790 sheet: -0.26 (0.26), residues: 325 loop : -2.31 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 315 TYR 0.017 0.001 TYR E 286 PHE 0.018 0.002 PHE B 181 TRP 0.022 0.002 TRP E 331 HIS 0.002 0.000 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00286 (17170) covalent geometry : angle 0.66450 (23450) SS BOND : bond 0.00248 ( 5) SS BOND : angle 0.33698 ( 10) hydrogen bonds : bond 0.05266 ( 790) hydrogen bonds : angle 4.61817 ( 2415) link_BETA1-4 : bond 0.00354 ( 20) link_BETA1-4 : angle 2.23360 ( 60) link_NAG-ASN : bond 0.01331 ( 9) link_NAG-ASN : angle 6.02845 ( 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 152 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 82 time to evaluate : 0.682 Fit side-chains REVERT: A 221 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7169 (tm) REVERT: A 320 TRP cc_start: 0.7664 (m100) cc_final: 0.6886 (m100) REVERT: B 320 TRP cc_start: 0.8036 (m100) cc_final: 0.7180 (m100) REVERT: C 320 TRP cc_start: 0.7867 (m100) cc_final: 0.6997 (m100) REVERT: D 221 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6860 (tt) REVERT: D 419 MET cc_start: 0.9105 (tmm) cc_final: 0.8876 (tmm) REVERT: E 221 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6986 (tt) REVERT: E 320 TRP cc_start: 0.7871 (m100) cc_final: 0.7094 (m100) REVERT: E 419 MET cc_start: 0.9169 (mmm) cc_final: 0.8595 (mmm) outliers start: 70 outliers final: 24 residues processed: 142 average time/residue: 0.1355 time to fit residues: 29.8250 Evaluate side-chains 96 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 221 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 116 TYR 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: 1.9990 chunk 74 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS B 158 HIS C 158 HIS D 158 HIS E 158 HIS ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.066394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.047745 restraints weight = 66741.538| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 4.08 r_work: 0.2796 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17204 Z= 0.278 Angle : 0.850 11.541 23547 Z= 0.411 Chirality : 0.047 0.427 2789 Planarity : 0.005 0.037 2830 Dihedral : 8.426 76.941 2895 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.87 % Allowed : 14.31 % Favored : 81.82 % 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: 0.10 (0.19), residues: 1935 helix: 2.06 (0.17), residues: 795 sheet: -0.83 (0.23), residues: 415 loop : -1.69 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 315 TYR 0.027 0.002 TYR B 286 PHE 0.013 0.002 PHE A 153 TRP 0.026 0.002 TRP A 168 HIS 0.004 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00622 (17170) covalent geometry : angle 0.82076 (23450) SS BOND : bond 0.00385 ( 5) SS BOND : angle 0.85444 ( 10) hydrogen bonds : bond 0.06057 ( 790) hydrogen bonds : angle 4.37353 ( 2415) link_BETA1-4 : bond 0.00479 ( 20) link_BETA1-4 : angle 2.19948 ( 60) link_NAG-ASN : bond 0.01252 ( 9) link_NAG-ASN : angle 5.81898 ( 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 142 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 72 time to evaluate : 0.756 Fit side-chains REVERT: A 235 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8559 (mmp) REVERT: A 320 TRP cc_start: 0.7898 (m100) cc_final: 0.7072 (m100) REVERT: B 223 TYR cc_start: 0.6015 (p90) cc_final: 0.5806 (p90) REVERT: B 320 TRP cc_start: 0.8205 (m100) cc_final: 0.7319 (m100) REVERT: C 210 MET cc_start: 0.9035 (tpp) cc_final: 0.8639 (tpt) REVERT: C 320 TRP cc_start: 0.7958 (m100) cc_final: 0.7054 (m100) REVERT: D 221 LEU cc_start: 0.7846 (tm) cc_final: 0.7627 (tm) REVERT: D 320 TRP cc_start: 0.7984 (m100) cc_final: 0.7056 (m100) REVERT: D 419 MET cc_start: 0.9255 (tmm) cc_final: 0.9019 (tmm) REVERT: E 286 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.8021 (t80) REVERT: E 320 TRP cc_start: 0.8060 (m100) cc_final: 0.7478 (m100) outliers start: 70 outliers final: 33 residues processed: 131 average time/residue: 0.1256 time to fit residues: 25.8079 Evaluate side-chains 96 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 61 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 235 MET 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 442 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 240 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 104 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 39 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 104 VAL Chi-restraints excluded: chain E residue 132 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 24 optimal weight: 8.9990 chunk 185 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.066289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.047539 restraints weight = 66825.699| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 4.09 r_work: 0.2783 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17204 Z= 0.198 Angle : 0.725 11.887 23547 Z= 0.337 Chirality : 0.044 0.407 2789 Planarity : 0.004 0.028 2830 Dihedral : 7.288 65.559 2895 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.97 % Allowed : 15.80 % Favored : 79.23 % 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: 0.45 (0.19), residues: 1935 helix: 2.56 (0.18), residues: 795 sheet: -0.62 (0.25), residues: 345 loop : -1.72 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 315 TYR 0.020 0.002 TYR C 286 PHE 0.008 0.001 PHE A 181 TRP 0.024 0.002 TRP D 168 HIS 0.003 0.001 HIS E 158 Details of bonding type rmsd covalent geometry : bond 0.00449 (17170) covalent geometry : angle 0.69282 (23450) SS BOND : bond 0.00172 ( 5) SS BOND : angle 0.69109 ( 10) hydrogen bonds : bond 0.05428 ( 790) hydrogen bonds : angle 4.07305 ( 2415) link_BETA1-4 : bond 0.00303 ( 20) link_BETA1-4 : angle 1.96055 ( 60) link_NAG-ASN : bond 0.01118 ( 9) link_NAG-ASN : angle 5.69527 ( 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 153 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 63 time to evaluate : 0.696 Fit side-chains REVERT: A 116 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8757 (m-80) REVERT: A 235 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8493 (mpp) REVERT: A 320 TRP cc_start: 0.7939 (m100) cc_final: 0.7105 (m100) REVERT: B 210 MET cc_start: 0.9157 (tpp) cc_final: 0.8771 (tpp) REVERT: B 320 TRP cc_start: 0.8224 (m100) cc_final: 0.7324 (m100) REVERT: C 210 MET cc_start: 0.8973 (tpp) cc_final: 0.8644 (tpt) REVERT: C 320 TRP cc_start: 0.8027 (m100) cc_final: 0.7114 (m100) REVERT: D 419 MET cc_start: 0.9275 (tmm) cc_final: 0.9061 (tmm) REVERT: E 320 TRP cc_start: 0.8108 (m100) cc_final: 0.7466 (m100) outliers start: 90 outliers final: 55 residues processed: 147 average time/residue: 0.0986 time to fit residues: 25.2181 Evaluate side-chains 113 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 56 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL 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 141 ASN Chi-restraints excluded: chain A residue 235 MET 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 307 LEU Chi-restraints excluded: chain A residue 323 HIS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain B residue 240 VAL 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 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 266 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 51 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 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 189 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 307 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 144 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.067173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.048739 restraints weight = 66179.119| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 4.10 r_work: 0.2814 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17204 Z= 0.131 Angle : 0.674 12.149 23547 Z= 0.308 Chirality : 0.043 0.339 2789 Planarity : 0.003 0.027 2830 Dihedral : 6.187 58.377 2895 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.20 % Allowed : 17.07 % Favored : 78.73 % 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: 2.85 (0.18), residues: 795 sheet: -0.33 (0.26), residues: 315 loop : -1.61 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 218 TYR 0.032 0.002 TYR B 223 PHE 0.015 0.001 PHE A 181 TRP 0.022 0.001 TRP C 187 HIS 0.001 0.000 HIS B 158 Details of bonding type rmsd covalent geometry : bond 0.00271 (17170) covalent geometry : angle 0.64169 (23450) SS BOND : bond 0.00094 ( 5) SS BOND : angle 0.44227 ( 10) hydrogen bonds : bond 0.05023 ( 790) hydrogen bonds : angle 3.79747 ( 2415) link_BETA1-4 : bond 0.00323 ( 20) link_BETA1-4 : angle 1.92664 ( 60) link_NAG-ASN : bond 0.01153 ( 9) link_NAG-ASN : angle 5.50375 ( 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 135 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 59 time to evaluate : 0.692 Fit side-chains REVERT: A 116 TYR cc_start: 0.9080 (OUTLIER) cc_final: 0.8636 (m-80) REVERT: A 235 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8492 (mpp) REVERT: A 320 TRP cc_start: 0.7941 (m100) cc_final: 0.7096 (m100) REVERT: A 443 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7976 (tt) REVERT: B 129 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9440 (pp) REVERT: B 210 MET cc_start: 0.9109 (tpp) cc_final: 0.8485 (tpt) REVERT: B 320 TRP cc_start: 0.8214 (m100) cc_final: 0.7320 (m100) REVERT: C 210 MET cc_start: 0.8936 (tpp) cc_final: 0.8512 (tpp) REVERT: C 320 TRP cc_start: 0.8025 (m100) cc_final: 0.7122 (m100) REVERT: D 419 MET cc_start: 0.9279 (tmm) cc_final: 0.9069 (tmm) REVERT: D 443 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8032 (tt) REVERT: E 129 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9445 (pp) REVERT: E 320 TRP cc_start: 0.8139 (m100) cc_final: 0.7511 (m100) REVERT: E 443 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7916 (tt) outliers start: 76 outliers final: 51 residues processed: 132 average time/residue: 0.1012 time to fit residues: 23.3050 Evaluate side-chains 110 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 52 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL 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 141 ASN Chi-restraints excluded: chain A residue 235 MET 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 39 VAL 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 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 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 189 LEU 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 269 VAL Chi-restraints excluded: chain C residue 309 HIS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 51 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 221 LEU 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 442 LEU Chi-restraints excluded: chain D residue 443 LEU 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 129 LEU 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 323 HIS Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 446 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 34 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 91 optimal weight: 0.0070 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.068838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.051682 restraints weight = 64437.577| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.32 r_work: 0.2814 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4737 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= 0.131 Angle : 0.661 12.333 23547 Z= 0.300 Chirality : 0.042 0.322 2789 Planarity : 0.003 0.027 2830 Dihedral : 5.378 58.269 2895 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.53 % Allowed : 16.57 % Favored : 78.90 % 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: 2.95 (0.18), residues: 800 sheet: -0.29 (0.26), residues: 315 loop : -1.64 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 315 TYR 0.019 0.001 TYR C 286 PHE 0.014 0.001 PHE A 144 TRP 0.013 0.001 TRP D 168 HIS 0.001 0.000 HIS C 158 Details of bonding type rmsd covalent geometry : bond 0.00279 (17170) covalent geometry : angle 0.63033 (23450) SS BOND : bond 0.00121 ( 5) SS BOND : angle 0.54062 ( 10) hydrogen bonds : bond 0.04770 ( 790) hydrogen bonds : angle 3.70720 ( 2415) link_BETA1-4 : bond 0.00290 ( 20) link_BETA1-4 : angle 1.77477 ( 60) link_NAG-ASN : bond 0.00985 ( 9) link_NAG-ASN : angle 5.38032 ( 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 137 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 55 time to evaluate : 0.773 Fit side-chains REVERT: A 235 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8449 (mpp) REVERT: A 320 TRP cc_start: 0.7950 (m100) cc_final: 0.7148 (m100) REVERT: A 443 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7961 (tt) REVERT: B 129 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9439 (pp) REVERT: B 210 MET cc_start: 0.9123 (tpp) cc_final: 0.8450 (tpt) REVERT: B 320 TRP cc_start: 0.8226 (m100) cc_final: 0.7336 (m100) REVERT: C 151 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8733 (pp) REVERT: C 210 MET cc_start: 0.8935 (tpp) cc_final: 0.8579 (tpp) REVERT: C 320 TRP cc_start: 0.8051 (m100) cc_final: 0.7153 (m100) REVERT: D 210 MET cc_start: 0.9157 (tpp) cc_final: 0.8922 (mmm) REVERT: D 320 TRP cc_start: 0.8021 (m100) cc_final: 0.7104 (m100) REVERT: D 419 MET cc_start: 0.9269 (tmm) cc_final: 0.9048 (tmm) REVERT: D 443 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8040 (tt) REVERT: E 320 TRP cc_start: 0.8132 (m100) cc_final: 0.7479 (m100) REVERT: E 443 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7921 (tt) outliers start: 82 outliers final: 56 residues processed: 133 average time/residue: 0.1060 time to fit residues: 23.8145 Evaluate side-chains 115 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 53 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 235 MET 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 39 VAL 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 260 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 323 HIS Chi-restraints excluded: chain B residue 442 LEU 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 151 LEU Chi-restraints excluded: chain C residue 167 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 309 HIS Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 51 VAL 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 238 ASP Chi-restraints excluded: chain D residue 260 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 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 189 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 120 optimal weight: 0.8980 chunk 179 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.068351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.051043 restraints weight = 64663.143| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.32 r_work: 0.2810 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17204 Z= 0.133 Angle : 0.653 12.190 23547 Z= 0.297 Chirality : 0.042 0.307 2789 Planarity : 0.003 0.028 2830 Dihedral : 5.091 58.072 2895 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 4.70 % Allowed : 16.57 % Favored : 78.73 % 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: 0.95 (0.20), residues: 1935 helix: 3.06 (0.18), residues: 790 sheet: -0.24 (0.26), residues: 315 loop : -1.56 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 315 TYR 0.032 0.001 TYR B 223 PHE 0.015 0.001 PHE A 144 TRP 0.014 0.001 TRP D 168 HIS 0.001 0.000 HIS B 158 Details of bonding type rmsd covalent geometry : bond 0.00283 (17170) covalent geometry : angle 0.62310 (23450) SS BOND : bond 0.00117 ( 5) SS BOND : angle 0.53410 ( 10) hydrogen bonds : bond 0.04649 ( 790) hydrogen bonds : angle 3.66328 ( 2415) link_BETA1-4 : bond 0.00298 ( 20) link_BETA1-4 : angle 1.62108 ( 60) link_NAG-ASN : bond 0.00973 ( 9) link_NAG-ASN : angle 5.30802 ( 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 138 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 53 time to evaluate : 0.656 Fit side-chains REVERT: A 151 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8743 (pp) REVERT: A 320 TRP cc_start: 0.7990 (m100) cc_final: 0.7195 (m100) REVERT: A 443 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7935 (tt) REVERT: B 116 TYR cc_start: 0.9208 (OUTLIER) cc_final: 0.8980 (m-80) REVERT: B 129 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9446 (pp) REVERT: B 151 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8751 (pp) REVERT: B 210 MET cc_start: 0.9152 (tpp) cc_final: 0.8490 (tpt) REVERT: B 320 TRP cc_start: 0.8227 (m100) cc_final: 0.7335 (m100) REVERT: C 151 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8746 (pp) REVERT: C 210 MET cc_start: 0.8959 (tpp) cc_final: 0.8607 (tpp) REVERT: C 320 TRP cc_start: 0.8061 (m100) cc_final: 0.7168 (m100) REVERT: D 210 MET cc_start: 0.9134 (tpp) cc_final: 0.8884 (mmm) REVERT: D 320 TRP cc_start: 0.8019 (m100) cc_final: 0.7094 (m100) REVERT: E 320 TRP cc_start: 0.8163 (m100) cc_final: 0.7488 (m100) REVERT: E 443 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7942 (tp) outliers start: 85 outliers final: 62 residues processed: 134 average time/residue: 0.0995 time to fit residues: 23.0173 Evaluate side-chains 120 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 51 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL 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 144 PHE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 221 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 39 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 116 TYR 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 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 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 132 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 167 LEU 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 446 LEU Chi-restraints excluded: chain D residue 39 VAL 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 167 LEU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 221 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 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 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 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 402 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 108 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 133 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 23 optimal weight: 0.0670 chunk 52 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 overall best weight: 1.2720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.067615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.049923 restraints weight = 66188.959| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 4.30 r_work: 0.2804 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17204 Z= 0.138 Angle : 0.668 13.503 23547 Z= 0.302 Chirality : 0.042 0.305 2789 Planarity : 0.003 0.028 2830 Dihedral : 4.999 57.913 2895 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.36 % Allowed : 17.18 % 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: 0.99 (0.20), residues: 1935 helix: 3.10 (0.18), residues: 790 sheet: -0.24 (0.26), residues: 315 loop : -1.53 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 315 TYR 0.021 0.001 TYR A 262 PHE 0.014 0.001 PHE A 144 TRP 0.015 0.001 TRP D 168 HIS 0.001 0.000 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00298 (17170) covalent geometry : angle 0.64037 (23450) SS BOND : bond 0.00110 ( 5) SS BOND : angle 0.56582 ( 10) hydrogen bonds : bond 0.04597 ( 790) hydrogen bonds : angle 3.63921 ( 2415) link_BETA1-4 : bond 0.00284 ( 20) link_BETA1-4 : angle 1.55592 ( 60) link_NAG-ASN : bond 0.00965 ( 9) link_NAG-ASN : angle 5.28774 ( 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 132 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 53 time to evaluate : 0.687 Fit side-chains REVERT: A 151 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8665 (pp) REVERT: A 291 MET cc_start: 0.8346 (tpp) cc_final: 0.7276 (tpp) REVERT: A 320 TRP cc_start: 0.8057 (m100) cc_final: 0.7237 (m100) REVERT: A 443 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7957 (tt) REVERT: B 116 TYR cc_start: 0.9183 (OUTLIER) cc_final: 0.8951 (m-80) REVERT: B 129 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9434 (pp) REVERT: B 151 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8703 (pp) REVERT: B 210 MET cc_start: 0.9119 (tpp) cc_final: 0.8414 (tpt) REVERT: B 320 TRP cc_start: 0.8292 (m100) cc_final: 0.7377 (m100) REVERT: C 151 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8653 (pp) REVERT: C 210 MET cc_start: 0.8948 (tpp) cc_final: 0.8588 (tpp) REVERT: C 320 TRP cc_start: 0.8100 (m100) cc_final: 0.7190 (m100) REVERT: D 210 MET cc_start: 0.9132 (tpp) cc_final: 0.8884 (mmm) REVERT: D 320 TRP cc_start: 0.8038 (m100) cc_final: 0.7098 (m100) REVERT: E 320 TRP cc_start: 0.8201 (m100) cc_final: 0.7539 (m100) REVERT: E 443 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7970 (tp) outliers start: 79 outliers final: 63 residues processed: 128 average time/residue: 0.0969 time to fit residues: 21.7809 Evaluate side-chains 120 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 50 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL 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 144 PHE Chi-restraints excluded: chain A residue 151 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 442 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 116 TYR 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 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 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 132 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 167 LEU 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 446 LEU Chi-restraints excluded: chain D residue 39 VAL 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 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 269 VAL Chi-restraints excluded: chain D residue 437 LEU 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 51 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 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: 3.9990 chunk 105 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 154 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 21 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.066554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049043 restraints weight = 65288.581| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 4.30 r_work: 0.2748 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.5445 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= 0.193 Angle : 0.697 11.934 23547 Z= 0.324 Chirality : 0.043 0.340 2789 Planarity : 0.003 0.030 2830 Dihedral : 5.284 58.390 2895 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.31 % Allowed : 17.62 % Favored : 78.07 % 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: 0.89 (0.20), residues: 1935 helix: 3.08 (0.18), residues: 790 sheet: -0.57 (0.26), residues: 325 loop : -1.52 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 218 TYR 0.026 0.002 TYR A 262 PHE 0.013 0.001 PHE A 144 TRP 0.045 0.002 TRP E 187 HIS 0.002 0.000 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00437 (17170) covalent geometry : angle 0.66945 (23450) SS BOND : bond 0.00154 ( 5) SS BOND : angle 0.76719 ( 10) hydrogen bonds : bond 0.04915 ( 790) hydrogen bonds : angle 3.79867 ( 2415) link_BETA1-4 : bond 0.00235 ( 20) link_BETA1-4 : angle 1.60055 ( 60) link_NAG-ASN : bond 0.00956 ( 9) link_NAG-ASN : angle 5.39262 ( 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 128 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 50 time to evaluate : 0.702 Fit side-chains REVERT: A 320 TRP cc_start: 0.8083 (m100) cc_final: 0.7244 (m100) REVERT: A 443 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8128 (tt) REVERT: B 116 TYR cc_start: 0.9209 (OUTLIER) cc_final: 0.8991 (m-80) REVERT: B 129 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9451 (pp) REVERT: B 151 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8728 (pp) REVERT: B 210 MET cc_start: 0.9224 (tpp) cc_final: 0.8601 (tpt) REVERT: B 320 TRP cc_start: 0.8314 (m100) cc_final: 0.7389 (m100) REVERT: C 210 MET cc_start: 0.8987 (tpp) cc_final: 0.8708 (tpp) REVERT: C 320 TRP cc_start: 0.8131 (m100) cc_final: 0.7209 (m100) REVERT: D 320 TRP cc_start: 0.8042 (m100) cc_final: 0.7143 (m100) REVERT: E 320 TRP cc_start: 0.8232 (m100) cc_final: 0.7595 (m100) outliers start: 78 outliers final: 60 residues processed: 124 average time/residue: 0.0971 time to fit residues: 21.3401 Evaluate side-chains 113 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 49 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL 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 144 PHE 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 39 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 116 TYR 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 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 446 LEU 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 132 VAL Chi-restraints excluded: chain C residue 167 LEU 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 446 LEU Chi-restraints excluded: chain D residue 39 VAL 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 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 437 LEU 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 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 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 18 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.067098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049694 restraints weight = 64622.510| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 4.29 r_work: 0.2767 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17204 Z= 0.143 Angle : 0.682 12.029 23547 Z= 0.309 Chirality : 0.042 0.315 2789 Planarity : 0.003 0.030 2830 Dihedral : 5.152 58.909 2895 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.70 % Allowed : 17.90 % Favored : 78.40 % 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: 0.94 (0.20), residues: 1935 helix: 3.12 (0.18), residues: 790 sheet: -0.45 (0.26), residues: 320 loop : -1.55 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 315 TYR 0.024 0.001 TYR A 262 PHE 0.013 0.001 PHE A 144 TRP 0.018 0.001 TRP D 168 HIS 0.001 0.000 HIS A 158 Details of bonding type rmsd covalent geometry : bond 0.00312 (17170) covalent geometry : angle 0.65470 (23450) SS BOND : bond 0.00113 ( 5) SS BOND : angle 0.58706 ( 10) hydrogen bonds : bond 0.04727 ( 790) hydrogen bonds : angle 3.65633 ( 2415) link_BETA1-4 : bond 0.00297 ( 20) link_BETA1-4 : angle 1.51556 ( 60) link_NAG-ASN : bond 0.00987 ( 9) link_NAG-ASN : angle 5.30021 ( 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 115 residues out of total 1825 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 48 time to evaluate : 0.706 Fit side-chains REVERT: A 291 MET cc_start: 0.8436 (tpp) cc_final: 0.7484 (tpp) REVERT: A 320 TRP cc_start: 0.8101 (m100) cc_final: 0.7261 (m100) REVERT: A 443 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8080 (tt) REVERT: B 116 TYR cc_start: 0.9196 (OUTLIER) cc_final: 0.8960 (m-80) REVERT: B 129 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9454 (pp) REVERT: B 151 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8672 (pp) REVERT: B 210 MET cc_start: 0.9223 (tpp) cc_final: 0.8644 (tpt) REVERT: B 320 TRP cc_start: 0.8331 (m100) cc_final: 0.7407 (m100) REVERT: C 210 MET cc_start: 0.8979 (tpp) cc_final: 0.8691 (tpp) REVERT: C 320 TRP cc_start: 0.8151 (m100) cc_final: 0.7237 (m100) REVERT: D 320 TRP cc_start: 0.8062 (m100) cc_final: 0.7171 (m100) REVERT: E 320 TRP cc_start: 0.8244 (m100) cc_final: 0.7361 (m100) outliers start: 67 outliers final: 61 residues processed: 114 average time/residue: 0.1016 time to fit residues: 20.2764 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 : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL 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 144 PHE 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 39 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 116 TYR 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 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 446 LEU 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 132 VAL Chi-restraints excluded: chain C residue 167 LEU 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 446 LEU Chi-restraints excluded: chain D residue 39 VAL 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 116 TYR 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 269 VAL Chi-restraints excluded: chain D residue 437 LEU 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 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 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 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: 0.0040 chunk 104 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 71 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.066447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.048651 restraints weight = 65048.991| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 4.01 r_work: 0.2808 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17204 Z= 0.124 Angle : 0.663 12.089 23547 Z= 0.299 Chirality : 0.042 0.301 2789 Planarity : 0.003 0.030 2830 Dihedral : 4.918 57.790 2895 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.92 % Allowed : 17.85 % 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: 0.97 (0.20), residues: 1935 helix: 3.06 (0.18), residues: 800 sheet: -0.35 (0.26), residues: 320 loop : -1.53 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 218 TYR 0.030 0.001 TYR B 223 PHE 0.013 0.001 PHE A 144 TRP 0.021 0.001 TRP E 187 HIS 0.001 0.000 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00260 (17170) covalent geometry : angle 0.63531 (23450) SS BOND : bond 0.00088 ( 5) SS BOND : angle 0.53787 ( 10) hydrogen bonds : bond 0.04482 ( 790) hydrogen bonds : angle 3.55306 ( 2415) link_BETA1-4 : bond 0.00328 ( 20) link_BETA1-4 : angle 1.47102 ( 60) link_NAG-ASN : bond 0.01009 ( 9) link_NAG-ASN : angle 5.23332 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3462.92 seconds wall clock time: 60 minutes 16.17 seconds (3616.17 seconds total)