Starting phenix.real_space_refine on Thu Feb 5 19:31:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9md2_48165/02_2026/9md2_48165.cif Found real_map, /net/cci-nas-00/data/ceres_data/9md2_48165/02_2026/9md2_48165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9md2_48165/02_2026/9md2_48165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9md2_48165/02_2026/9md2_48165.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9md2_48165/02_2026/9md2_48165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9md2_48165/02_2026/9md2_48165.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 132 5.16 5 C 12184 2.51 5 N 3280 2.21 5 O 3936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19536 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3000 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 373} Chain: "H" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "B" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3000 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 373} Chain: "E" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "I" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "C" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3000 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 373} Chain: "F" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "J" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3000 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 373} Chain: "G" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "K" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' CA': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.85, per 1000 atoms: 0.25 Number of scatterers: 19536 At special positions: 0 Unit cell: (139.925, 139.925, 89.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 132 16.00 O 3936 8.00 N 3280 7.00 C 12184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.03 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 193 " distance=2.03 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=2.03 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.03 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " ALPHA1-6 " BMA M 3 " - " MAN M 5 " " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 5 " " BMA P 3 " - " MAN P 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG A 501 " - " ASN A 146 " " NAG A 502 " - " ASN A 367 " " NAG A 504 " - " ASN A 234 " " NAG A 505 " - " ASN A 309 " " NAG B 501 " - " ASN B 146 " " NAG B 502 " - " ASN B 367 " " NAG B 504 " - " ASN B 234 " " NAG B 505 " - " ASN B 309 " " NAG C 501 " - " ASN C 146 " " NAG C 502 " - " ASN C 367 " " NAG C 504 " - " ASN C 234 " " NAG C 505 " - " ASN C 309 " " NAG D 501 " - " ASN D 146 " " NAG D 502 " - " ASN D 367 " " NAG D 504 " - " ASN D 234 " " NAG D 505 " - " ASN D 309 " " NAG M 1 " - " ASN A 200 " " NAG N 1 " - " ASN B 200 " " NAG O 1 " - " ASN C 200 " " NAG P 1 " - " ASN D 200 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 853.2 milliseconds 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4424 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 52 sheets defined 2.4% alpha, 43.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 104 through 110 removed outlier: 3.609A pdb=" N LEU A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.759A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.657A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.757A pdb=" N THR E 87 " --> pdb=" O SER E 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.641A pdb=" N ALA C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.800A pdb=" N SER C 145 " --> pdb=" O ASN C 142 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASN C 146 " --> pdb=" O GLY C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 142 through 146' Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.758A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 removed outlier: 3.628A pdb=" N LEU D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.770A pdb=" N SER D 145 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN D 146 " --> pdb=" O GLY D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 146' Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.762A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 3.724A pdb=" N GLY A 96 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.969A pdb=" N TRP A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR A 138 " --> pdb=" O TRP A 115 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A 158 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A 172 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.742A pdb=" N ASP A 213 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.505A pdb=" N ILE A 233 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 removed outlier: 6.102A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 281 removed outlier: 5.029A pdb=" N CYS A 278 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 290 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N CYS A 280 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ARG A 288 " --> pdb=" O CYS A 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 355 removed outlier: 4.755A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 360 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LEU A 372 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL A 398 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N TYR A 374 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VAL A 396 " --> pdb=" O TYR A 374 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR A 376 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG A 394 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.815A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 57 through 58 removed outlier: 6.598A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N GLY H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY H 95 " --> pdb=" O GLY H 33 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 57 through 58 removed outlier: 6.598A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N GLY H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY H 95 " --> pdb=" O GLY H 33 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.887A pdb=" N ASP L 70 " --> pdb=" O TYR L 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.012A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.770A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 96 through 102 removed outlier: 3.735A pdb=" N GLY B 96 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 445 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.977A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.550A pdb=" N SER B 179 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP B 213 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 224 through 225 removed outlier: 3.517A pdb=" N THR B 236 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 233 " --> pdb=" O THR B 236 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 224 through 225 removed outlier: 6.106A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 276 through 281 removed outlier: 5.073A pdb=" N CYS B 278 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 290 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N CYS B 280 " --> pdb=" O ARG B 288 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ARG B 288 " --> pdb=" O CYS B 280 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 352 through 355 removed outlier: 4.708A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY B 363 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL B 360 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 372 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N GLU B 399 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS B 378 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASN B 393 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.785A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 80 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 57 through 58 removed outlier: 6.599A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET E 34 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLY E 33 " --> pdb=" O GLY E 95 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY E 95 " --> pdb=" O GLY E 33 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 57 through 58 removed outlier: 6.599A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET E 34 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLY E 33 " --> pdb=" O GLY E 95 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY E 95 " --> pdb=" O GLY E 33 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.885A pdb=" N ASP I 70 " --> pdb=" O TYR I 67 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 12 removed outlier: 7.013A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'I' and resid 45 through 48 removed outlier: 6.791A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 96 through 102 removed outlier: 3.704A pdb=" N GLY C 96 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL C 445 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS C 102 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ARG C 420 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 121 through 124 removed outlier: 3.587A pdb=" N ALA C 133 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C 158 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG C 172 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 179 through 184 removed outlier: 3.749A pdb=" N ASP C 213 " --> pdb=" O PHE C 205 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR C 207 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 223 through 225 removed outlier: 3.503A pdb=" N THR C 236 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 233 " --> pdb=" O THR C 236 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 223 through 225 removed outlier: 6.114A pdb=" N GLU C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 276 through 281 removed outlier: 5.023A pdb=" N CYS C 278 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL C 290 " --> pdb=" O CYS C 278 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N CYS C 280 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ARG C 288 " --> pdb=" O CYS C 280 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 352 through 355 removed outlier: 4.734A pdb=" N TRP C 352 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 363 " --> pdb=" O TRP C 352 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LEU C 372 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL C 398 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TYR C 374 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N VAL C 396 " --> pdb=" O TYR C 374 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR C 376 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG C 394 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.511A pdb=" N VAL F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU F 80 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 57 through 58 removed outlier: 6.598A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET F 34 " --> pdb=" O THR F 50 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N GLY F 33 " --> pdb=" O GLY F 95 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY F 95 " --> pdb=" O GLY F 33 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 57 through 58 removed outlier: 6.598A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET F 34 " --> pdb=" O THR F 50 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N GLY F 33 " --> pdb=" O GLY F 95 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY F 95 " --> pdb=" O GLY F 33 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.871A pdb=" N ASP J 70 " --> pdb=" O TYR J 67 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.986A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.756A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 96 through 102 removed outlier: 3.716A pdb=" N GLY D 96 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL D 445 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 115 through 124 removed outlier: 5.036A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA D 133 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU D 158 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG D 172 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 179 through 184 removed outlier: 3.753A pdb=" N ASP D 213 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LEU D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 223 through 225 removed outlier: 3.619A pdb=" N ILE D 233 " --> pdb=" O THR D 236 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 223 through 225 removed outlier: 6.148A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 276 through 281 removed outlier: 5.011A pdb=" N CYS D 278 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL D 290 " --> pdb=" O CYS D 278 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N CYS D 280 " --> pdb=" O ARG D 288 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ARG D 288 " --> pdb=" O CYS D 280 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 352 through 355 removed outlier: 4.712A pdb=" N TRP D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY D 363 " --> pdb=" O TRP D 352 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 360 " --> pdb=" O VAL D 379 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU D 372 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL D 398 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N TYR D 374 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL D 396 " --> pdb=" O TYR D 374 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR D 376 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG D 394 " --> pdb=" O THR D 376 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.817A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU G 80 " --> pdb=" O LEU G 20 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 57 through 58 removed outlier: 6.602A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET G 34 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY G 33 " --> pdb=" O GLY G 95 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY G 95 " --> pdb=" O GLY G 33 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 57 through 58 removed outlier: 6.602A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N MET G 34 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY G 33 " --> pdb=" O GLY G 95 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY G 95 " --> pdb=" O GLY G 33 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.886A pdb=" N ASP K 70 " --> pdb=" O TYR K 67 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 10 through 12 removed outlier: 7.009A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.769A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 618 hydrogen bonds defined for protein. 1653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.99 Time building geometry restraints manager: 2.39 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: 6225 1.34 - 1.46: 4625 1.46 - 1.58: 8954 1.58 - 1.70: 0 1.70 - 1.81: 176 Bond restraints: 19980 Sorted by residual: bond pdb=" CB TYR D 155 " pdb=" CG TYR D 155 " ideal model delta sigma weight residual 1.512 1.492 0.020 2.20e-02 2.07e+03 8.39e-01 bond pdb=" C1 MAN N 5 " pdb=" O5 MAN N 5 " ideal model delta sigma weight residual 1.399 1.416 -0.017 2.00e-02 2.50e+03 7.32e-01 bond pdb=" CB TYR B 155 " pdb=" CG TYR B 155 " ideal model delta sigma weight residual 1.512 1.493 0.019 2.20e-02 2.07e+03 7.24e-01 bond pdb=" C1 MAN M 5 " pdb=" O5 MAN M 5 " ideal model delta sigma weight residual 1.399 1.416 -0.017 2.00e-02 2.50e+03 6.91e-01 bond pdb=" C1 MAN P 5 " pdb=" O5 MAN P 5 " ideal model delta sigma weight residual 1.399 1.415 -0.016 2.00e-02 2.50e+03 6.50e-01 ... (remaining 19975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 26603 1.66 - 3.31: 415 3.31 - 4.97: 75 4.97 - 6.63: 7 6.63 - 8.28: 8 Bond angle restraints: 27108 Sorted by residual: angle pdb=" CA TYR D 155 " pdb=" CB TYR D 155 " pdb=" CG TYR D 155 " ideal model delta sigma weight residual 113.90 108.60 5.30 1.80e+00 3.09e-01 8.66e+00 angle pdb=" CA TYR B 155 " pdb=" CB TYR B 155 " pdb=" CG TYR B 155 " ideal model delta sigma weight residual 113.90 108.61 5.29 1.80e+00 3.09e-01 8.63e+00 angle pdb=" N VAL D 263 " pdb=" CA VAL D 263 " pdb=" C VAL D 263 " ideal model delta sigma weight residual 112.96 110.30 2.66 1.00e+00 1.00e+00 7.06e+00 angle pdb=" CA PRO C 459 " pdb=" C PRO C 459 " pdb=" N ASP C 460 " ideal model delta sigma weight residual 115.12 118.16 -3.04 1.25e+00 6.40e-01 5.90e+00 angle pdb=" CA LEU E 11 " pdb=" CB LEU E 11 " pdb=" CG LEU E 11 " ideal model delta sigma weight residual 116.30 124.58 -8.28 3.50e+00 8.16e-02 5.60e+00 ... (remaining 27103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 11284 17.91 - 35.83: 774 35.83 - 53.74: 174 53.74 - 71.66: 25 71.66 - 89.57: 19 Dihedral angle restraints: 12276 sinusoidal: 5280 harmonic: 6996 Sorted by residual: dihedral pdb=" CB CYS D 92 " pdb=" SG CYS D 92 " pdb=" SG CYS D 417 " pdb=" CB CYS D 417 " ideal model delta sinusoidal sigma weight residual 93.00 19.66 73.34 1 1.00e+01 1.00e-02 6.85e+01 dihedral pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " pdb=" SG CYS A 417 " pdb=" CB CYS A 417 " ideal model delta sinusoidal sigma weight residual 93.00 19.90 73.10 1 1.00e+01 1.00e-02 6.81e+01 dihedral pdb=" CB CYS B 92 " pdb=" SG CYS B 92 " pdb=" SG CYS B 417 " pdb=" CB CYS B 417 " ideal model delta sinusoidal sigma weight residual 93.00 20.71 72.29 1 1.00e+01 1.00e-02 6.68e+01 ... (remaining 12273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2055 0.035 - 0.070: 653 0.070 - 0.105: 218 0.105 - 0.140: 93 0.140 - 0.175: 9 Chirality restraints: 3028 Sorted by residual: chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.10 -0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.10 -0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.10 -0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 3025 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 125 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO C 126 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 126 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 126 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 125 " 0.041 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO B 126 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 125 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.30e+00 pdb=" N PRO D 126 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 126 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 126 " -0.032 5.00e-02 4.00e+02 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3367 2.77 - 3.30: 17745 3.30 - 3.84: 33783 3.84 - 4.37: 41141 4.37 - 4.90: 74093 Nonbonded interactions: 170129 Sorted by model distance: nonbonded pdb=" NE2 HIS D 150 " pdb=" OG SER G 100A" model vdw 2.238 3.120 nonbonded pdb=" NE2 HIS C 150 " pdb=" OG SER F 100A" model vdw 2.238 3.120 nonbonded pdb=" OG SER C 269 " pdb=" O ILE C 312 " model vdw 2.247 3.040 nonbonded pdb=" OG SER D 269 " pdb=" O ILE D 312 " model vdw 2.251 3.040 nonbonded pdb=" OG SER A 269 " pdb=" O ILE A 312 " model vdw 2.257 3.040 ... (remaining 170124 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.160 Find NCS groups from input model: 0.360 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20064 Z= 0.113 Angle : 0.581 8.285 27304 Z= 0.292 Chirality : 0.042 0.175 3028 Planarity : 0.005 0.064 3436 Dihedral : 12.769 89.570 7720 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.88 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.16), residues: 2444 helix: -2.83 (0.86), residues: 24 sheet: -0.43 (0.18), residues: 916 loop : -1.63 (0.15), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 172 TYR 0.024 0.001 TYR D 155 PHE 0.011 0.001 PHE C 354 TRP 0.024 0.001 TRP F 100C HIS 0.005 0.001 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.00247 (19980) covalent geometry : angle 0.55001 (27108) SS BOND : bond 0.00198 ( 44) SS BOND : angle 1.32926 ( 88) hydrogen bonds : bond 0.25124 ( 566) hydrogen bonds : angle 11.67659 ( 1653) Misc. bond : bond 0.00037 ( 4) link_ALPHA1-3 : bond 0.01060 ( 4) link_ALPHA1-3 : angle 1.51253 ( 12) link_ALPHA1-6 : bond 0.01037 ( 4) link_ALPHA1-6 : angle 2.52728 ( 12) link_BETA1-4 : bond 0.00497 ( 8) link_BETA1-4 : angle 1.23636 ( 24) link_NAG-ASN : bond 0.00277 ( 20) link_NAG-ASN : angle 3.44003 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 463 ASP cc_start: 0.7493 (m-30) cc_final: 0.7275 (m-30) REVERT: I 61 ARG cc_start: 0.7594 (ttp-170) cc_final: 0.7363 (ttp80) REVERT: J 61 ARG cc_start: 0.7622 (ttp-170) cc_final: 0.7363 (ttp80) REVERT: G 32 TYR cc_start: 0.8644 (m-80) cc_final: 0.8439 (m-80) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1218 time to fit residues: 56.4094 Evaluate side-chains 250 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.0870 chunk 235 optimal weight: 5.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN L 38 GLN B 226 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 226 GLN C 395 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN J 38 GLN D 226 GLN D 395 GLN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN K 38 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.134745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.107491 restraints weight = 21280.453| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.57 r_work: 0.3108 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20064 Z= 0.148 Angle : 0.592 6.671 27304 Z= 0.307 Chirality : 0.045 0.187 3028 Planarity : 0.005 0.056 3436 Dihedral : 6.179 44.550 3428 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.35 % Rotamer: Outliers : 0.42 % Allowed : 8.29 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.17), residues: 2444 helix: -2.41 (0.85), residues: 24 sheet: -0.20 (0.18), residues: 920 loop : -1.52 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 172 TYR 0.018 0.001 TYR B 155 PHE 0.012 0.001 PHE C 354 TRP 0.019 0.001 TRP F 100C HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00333 (19980) covalent geometry : angle 0.57026 (27108) SS BOND : bond 0.00280 ( 44) SS BOND : angle 1.10640 ( 88) hydrogen bonds : bond 0.05402 ( 566) hydrogen bonds : angle 8.56342 ( 1653) Misc. bond : bond 0.00022 ( 4) link_ALPHA1-3 : bond 0.01062 ( 4) link_ALPHA1-3 : angle 1.42707 ( 12) link_ALPHA1-6 : bond 0.01021 ( 4) link_ALPHA1-6 : angle 2.66001 ( 12) link_BETA1-4 : bond 0.00563 ( 8) link_BETA1-4 : angle 1.27340 ( 24) link_NAG-ASN : bond 0.00297 ( 20) link_NAG-ASN : angle 2.88785 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 264 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: L 61 ARG cc_start: 0.7396 (ttp80) cc_final: 0.7125 (ttp80) REVERT: I 61 ARG cc_start: 0.7511 (ttp-170) cc_final: 0.7258 (ttp80) REVERT: C 86 ASN cc_start: 0.8415 (m-40) cc_final: 0.8156 (m-40) REVERT: J 13 MET cc_start: 0.6932 (ppp) cc_final: 0.6264 (ppp) REVERT: J 61 ARG cc_start: 0.7548 (ttp-170) cc_final: 0.7173 (ttp80) REVERT: D 86 ASN cc_start: 0.8458 (m-40) cc_final: 0.8200 (m-40) REVERT: K 61 ARG cc_start: 0.7408 (ttp80) cc_final: 0.7139 (ttp80) outliers start: 9 outliers final: 9 residues processed: 267 average time/residue: 0.1191 time to fit residues: 52.5204 Evaluate side-chains 255 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 246 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 443 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 75 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 182 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 ASN C 173 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.128565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.101493 restraints weight = 21683.155| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.57 r_work: 0.3036 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20064 Z= 0.222 Angle : 0.646 7.013 27304 Z= 0.331 Chirality : 0.048 0.212 3028 Planarity : 0.005 0.052 3436 Dihedral : 6.408 39.566 3428 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.24 % Favored : 94.60 % Rotamer: Outliers : 1.93 % Allowed : 10.69 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.16), residues: 2444 helix: -1.76 (1.03), residues: 24 sheet: -0.20 (0.18), residues: 876 loop : -1.59 (0.15), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 156 TYR 0.015 0.001 TYR B 121 PHE 0.015 0.002 PHE D 132 TRP 0.023 0.002 TRP H 100C HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00526 (19980) covalent geometry : angle 0.61887 (27108) SS BOND : bond 0.00322 ( 44) SS BOND : angle 1.37612 ( 88) hydrogen bonds : bond 0.04379 ( 566) hydrogen bonds : angle 7.59280 ( 1653) Misc. bond : bond 0.00042 ( 4) link_ALPHA1-3 : bond 0.01067 ( 4) link_ALPHA1-3 : angle 1.68067 ( 12) link_ALPHA1-6 : bond 0.00708 ( 4) link_ALPHA1-6 : angle 2.28230 ( 12) link_BETA1-4 : bond 0.00394 ( 8) link_BETA1-4 : angle 1.40512 ( 24) link_NAG-ASN : bond 0.00411 ( 20) link_NAG-ASN : angle 3.41517 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 253 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: L 13 MET cc_start: 0.6952 (ppp) cc_final: 0.6519 (ppp) REVERT: L 23 CYS cc_start: 0.7659 (t) cc_final: 0.7242 (t) REVERT: L 61 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7263 (ttp80) REVERT: I 13 MET cc_start: 0.6974 (ppp) cc_final: 0.6518 (ppp) REVERT: I 61 ARG cc_start: 0.7571 (ttp-170) cc_final: 0.7257 (ttp80) REVERT: C 86 ASN cc_start: 0.8504 (m-40) cc_final: 0.8257 (m-40) REVERT: J 61 ARG cc_start: 0.7580 (ttp-170) cc_final: 0.7252 (ttp80) REVERT: D 86 ASN cc_start: 0.8504 (m-40) cc_final: 0.8251 (m-40) REVERT: D 103 ASP cc_start: 0.8222 (t70) cc_final: 0.8005 (t70) REVERT: D 293 ASP cc_start: 0.8230 (t70) cc_final: 0.7944 (t70) REVERT: K 13 MET cc_start: 0.6983 (ppp) cc_final: 0.6549 (ppp) REVERT: K 23 CYS cc_start: 0.7624 (t) cc_final: 0.7212 (t) REVERT: K 61 ARG cc_start: 0.7511 (ttp80) cc_final: 0.7260 (ttp80) outliers start: 41 outliers final: 40 residues processed: 269 average time/residue: 0.1205 time to fit residues: 52.8471 Evaluate side-chains 268 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 228 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain K residue 72 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 63 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 0.1980 chunk 223 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 170 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.135067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.107355 restraints weight = 21150.678| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.69 r_work: 0.2954 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20064 Z= 0.127 Angle : 0.550 6.584 27304 Z= 0.280 Chirality : 0.044 0.195 3028 Planarity : 0.004 0.058 3436 Dihedral : 5.925 35.413 3428 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.46 % Favored : 95.38 % Rotamer: Outliers : 1.79 % Allowed : 13.04 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.16), residues: 2444 helix: -1.44 (1.08), residues: 24 sheet: -0.19 (0.18), residues: 888 loop : -1.48 (0.15), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 156 TYR 0.010 0.001 TYR D 155 PHE 0.011 0.001 PHE C 354 TRP 0.017 0.001 TRP C 178 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00288 (19980) covalent geometry : angle 0.52585 (27108) SS BOND : bond 0.00182 ( 44) SS BOND : angle 1.07067 ( 88) hydrogen bonds : bond 0.03649 ( 566) hydrogen bonds : angle 7.07884 ( 1653) Misc. bond : bond 0.00033 ( 4) link_ALPHA1-3 : bond 0.01061 ( 4) link_ALPHA1-3 : angle 1.39752 ( 12) link_ALPHA1-6 : bond 0.00876 ( 4) link_ALPHA1-6 : angle 2.78670 ( 12) link_BETA1-4 : bond 0.00490 ( 8) link_BETA1-4 : angle 1.26129 ( 24) link_NAG-ASN : bond 0.00313 ( 20) link_NAG-ASN : angle 2.92256 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 240 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: H 38 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7154 (ptp-170) REVERT: L 13 MET cc_start: 0.6946 (ppp) cc_final: 0.6265 (ppp) REVERT: L 61 ARG cc_start: 0.7462 (ttp80) cc_final: 0.7212 (ttp80) REVERT: B 86 ASN cc_start: 0.8500 (m-40) cc_final: 0.8265 (m-40) REVERT: E 38 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7181 (ptp-170) REVERT: I 13 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6321 (ppp) REVERT: I 61 ARG cc_start: 0.7474 (ttp-170) cc_final: 0.7204 (ttp80) REVERT: C 86 ASN cc_start: 0.8480 (m-40) cc_final: 0.8239 (m-40) REVERT: F 38 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7153 (ptp-170) REVERT: J 61 ARG cc_start: 0.7465 (ttp-170) cc_final: 0.7125 (ttp80) REVERT: D 86 ASN cc_start: 0.8495 (m-40) cc_final: 0.8252 (m-40) REVERT: D 103 ASP cc_start: 0.8215 (t70) cc_final: 0.7983 (t70) REVERT: G 38 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7154 (ptp-170) REVERT: K 13 MET cc_start: 0.6956 (ppp) cc_final: 0.6270 (ppp) REVERT: K 61 ARG cc_start: 0.7472 (ttp80) cc_final: 0.7225 (ttp80) outliers start: 38 outliers final: 27 residues processed: 262 average time/residue: 0.1147 time to fit residues: 49.3844 Evaluate side-chains 257 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain K residue 72 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 200 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 181 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 233 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.144398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.123018 restraints weight = 20815.808| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.41 r_work: 0.2921 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20064 Z= 0.152 Angle : 0.570 7.044 27304 Z= 0.288 Chirality : 0.045 0.198 3028 Planarity : 0.004 0.059 3436 Dihedral : 5.912 36.746 3428 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.54 % Favored : 95.29 % Rotamer: Outliers : 2.78 % Allowed : 13.14 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.17), residues: 2444 helix: -1.18 (1.11), residues: 24 sheet: -0.29 (0.17), residues: 948 loop : -1.40 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 156 TYR 0.010 0.001 TYR B 121 PHE 0.013 0.001 PHE C 410 TRP 0.015 0.001 TRP C 178 HIS 0.003 0.001 HIS B 191 Details of bonding type rmsd covalent geometry : bond 0.00354 (19980) covalent geometry : angle 0.54250 (27108) SS BOND : bond 0.00225 ( 44) SS BOND : angle 1.19166 ( 88) hydrogen bonds : bond 0.03615 ( 566) hydrogen bonds : angle 6.85139 ( 1653) Misc. bond : bond 0.00030 ( 4) link_ALPHA1-3 : bond 0.01030 ( 4) link_ALPHA1-3 : angle 1.46070 ( 12) link_ALPHA1-6 : bond 0.00844 ( 4) link_ALPHA1-6 : angle 2.52784 ( 12) link_BETA1-4 : bond 0.00493 ( 8) link_BETA1-4 : angle 1.26849 ( 24) link_NAG-ASN : bond 0.00491 ( 20) link_NAG-ASN : angle 3.22316 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 241 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: H 38 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.7455 (ptp-170) REVERT: L 13 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6219 (ppp) REVERT: L 61 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7441 (ttp80) REVERT: B 86 ASN cc_start: 0.8663 (m-40) cc_final: 0.8460 (m-40) REVERT: B 325 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.8037 (m) REVERT: E 38 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.7381 (ptp-170) REVERT: I 13 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6308 (ppp) REVERT: I 61 ARG cc_start: 0.7658 (ttp-170) cc_final: 0.7319 (ttp80) REVERT: C 293 ASP cc_start: 0.8265 (t70) cc_final: 0.8056 (t70) REVERT: F 38 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.7420 (ptp-170) REVERT: J 61 ARG cc_start: 0.7653 (ttp-170) cc_final: 0.7358 (ttp80) REVERT: D 86 ASN cc_start: 0.8645 (m-40) cc_final: 0.8434 (m-40) REVERT: D 103 ASP cc_start: 0.8298 (t70) cc_final: 0.8087 (t70) REVERT: D 293 ASP cc_start: 0.8223 (t70) cc_final: 0.8000 (t70) REVERT: G 38 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7382 (ptp-170) REVERT: K 13 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.6270 (ppp) REVERT: K 61 ARG cc_start: 0.7703 (ttp80) cc_final: 0.7441 (ttp80) outliers start: 59 outliers final: 45 residues processed: 268 average time/residue: 0.1200 time to fit residues: 52.0465 Evaluate side-chains 285 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain K residue 13 MET Chi-restraints excluded: chain K residue 72 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 91 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 HIS ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 184 HIS ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 HIS ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.120341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.096047 restraints weight = 21889.066| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.36 r_work: 0.2835 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20064 Z= 0.221 Angle : 0.620 7.283 27304 Z= 0.315 Chirality : 0.047 0.211 3028 Planarity : 0.004 0.059 3436 Dihedral : 6.291 40.153 3428 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.36 % Favored : 94.44 % Rotamer: Outliers : 3.25 % Allowed : 13.28 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.17), residues: 2444 helix: -1.26 (1.11), residues: 24 sheet: -0.40 (0.17), residues: 996 loop : -1.43 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 172 TYR 0.013 0.001 TYR D 121 PHE 0.015 0.002 PHE D 132 TRP 0.014 0.002 TRP G 100C HIS 0.005 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00527 (19980) covalent geometry : angle 0.59184 (27108) SS BOND : bond 0.00319 ( 44) SS BOND : angle 1.45842 ( 88) hydrogen bonds : bond 0.03789 ( 566) hydrogen bonds : angle 6.92581 ( 1653) Misc. bond : bond 0.00044 ( 4) link_ALPHA1-3 : bond 0.01029 ( 4) link_ALPHA1-3 : angle 1.61254 ( 12) link_ALPHA1-6 : bond 0.00696 ( 4) link_ALPHA1-6 : angle 2.33886 ( 12) link_BETA1-4 : bond 0.00426 ( 8) link_BETA1-4 : angle 1.36382 ( 24) link_NAG-ASN : bond 0.00466 ( 20) link_NAG-ASN : angle 3.38616 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 241 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 325 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8103 (m) REVERT: H 38 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7254 (ptp-170) REVERT: L 13 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6218 (ppp) REVERT: L 34 ASN cc_start: 0.8954 (m-40) cc_final: 0.8697 (m-40) REVERT: L 61 ARG cc_start: 0.7690 (ttp80) cc_final: 0.7392 (ttp80) REVERT: B 86 ASN cc_start: 0.8616 (m-40) cc_final: 0.8408 (m-40) REVERT: B 293 ASP cc_start: 0.8173 (t70) cc_final: 0.7954 (t70) REVERT: B 325 THR cc_start: 0.8223 (OUTLIER) cc_final: 0.7968 (m) REVERT: E 38 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7315 (ptp-170) REVERT: I 13 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6319 (ppp) REVERT: I 34 ASN cc_start: 0.8937 (m-40) cc_final: 0.8709 (m-40) REVERT: I 61 ARG cc_start: 0.7678 (ttp-170) cc_final: 0.7348 (ttp80) REVERT: C 86 ASN cc_start: 0.8596 (m-40) cc_final: 0.8392 (m-40) REVERT: C 292 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.7746 (ttm170) REVERT: C 325 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8086 (m) REVERT: F 38 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7284 (ptp-170) REVERT: J 34 ASN cc_start: 0.8974 (m-40) cc_final: 0.8732 (m-40) REVERT: J 61 ARG cc_start: 0.7662 (ttp-170) cc_final: 0.7335 (ttp80) REVERT: D 293 ASP cc_start: 0.8160 (t70) cc_final: 0.7953 (t70) REVERT: G 38 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7309 (ptp-170) REVERT: K 13 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6255 (ppp) REVERT: K 34 ASN cc_start: 0.8954 (m-40) cc_final: 0.8707 (m-40) REVERT: K 61 ARG cc_start: 0.7706 (ttp80) cc_final: 0.7396 (ttp80) outliers start: 69 outliers final: 48 residues processed: 275 average time/residue: 0.1235 time to fit residues: 54.9592 Evaluate side-chains 287 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 228 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 457 SER Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain J residue 30 ASP Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain K residue 13 MET Chi-restraints excluded: chain K residue 72 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 160 optimal weight: 0.0170 chunk 102 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 187 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.125493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.099253 restraints weight = 21661.910| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.49 r_work: 0.3023 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20064 Z= 0.122 Angle : 0.552 7.595 27304 Z= 0.280 Chirality : 0.044 0.202 3028 Planarity : 0.004 0.061 3436 Dihedral : 5.867 35.810 3428 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.83 % Favored : 94.93 % Rotamer: Outliers : 2.68 % Allowed : 14.41 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.17), residues: 2444 helix: -1.23 (1.06), residues: 24 sheet: -0.29 (0.17), residues: 948 loop : -1.33 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 156 TYR 0.010 0.001 TYR B 121 PHE 0.012 0.001 PHE A 410 TRP 0.017 0.001 TRP C 178 HIS 0.003 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00275 (19980) covalent geometry : angle 0.52735 (27108) SS BOND : bond 0.00183 ( 44) SS BOND : angle 1.15296 ( 88) hydrogen bonds : bond 0.03373 ( 566) hydrogen bonds : angle 6.57813 ( 1653) Misc. bond : bond 0.00032 ( 4) link_ALPHA1-3 : bond 0.01127 ( 4) link_ALPHA1-3 : angle 1.39996 ( 12) link_ALPHA1-6 : bond 0.00944 ( 4) link_ALPHA1-6 : angle 2.76726 ( 12) link_BETA1-4 : bond 0.00495 ( 8) link_BETA1-4 : angle 1.25472 ( 24) link_NAG-ASN : bond 0.00592 ( 20) link_NAG-ASN : angle 2.91666 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 CYS cc_start: 0.6658 (m) cc_final: 0.6026 (m) REVERT: A 325 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8121 (m) REVERT: H 38 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7156 (ptp-170) REVERT: L 13 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.6284 (ppp) REVERT: L 61 ARG cc_start: 0.7688 (ttp80) cc_final: 0.7486 (ttp80) REVERT: E 38 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7208 (ptp-170) REVERT: I 13 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6362 (ppp) REVERT: I 61 ARG cc_start: 0.7676 (ttp-170) cc_final: 0.7383 (ttp80) REVERT: C 294 ASN cc_start: 0.8586 (t0) cc_final: 0.8085 (t0) REVERT: C 318 CYS cc_start: 0.6504 (m) cc_final: 0.5854 (m) REVERT: F 38 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7192 (ptp-170) REVERT: J 61 ARG cc_start: 0.7660 (ttp-170) cc_final: 0.7364 (ttp80) REVERT: D 292 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8119 (ttm170) REVERT: D 293 ASP cc_start: 0.8094 (t70) cc_final: 0.7884 (t70) REVERT: D 318 CYS cc_start: 0.6533 (m) cc_final: 0.5884 (m) REVERT: G 38 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7154 (ptp-170) REVERT: K 13 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6314 (ppp) REVERT: K 61 ARG cc_start: 0.7708 (ttp80) cc_final: 0.7489 (ttp80) outliers start: 57 outliers final: 33 residues processed: 266 average time/residue: 0.1153 time to fit residues: 49.6817 Evaluate side-chains 265 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain K residue 13 MET Chi-restraints excluded: chain K residue 72 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 114 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 177 optimal weight: 0.7980 chunk 1 optimal weight: 0.0670 chunk 0 optimal weight: 4.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 199 ASN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 441 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.138414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.111075 restraints weight = 21158.610| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.70 r_work: 0.2827 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20064 Z= 0.119 Angle : 0.551 10.714 27304 Z= 0.278 Chirality : 0.044 0.191 3028 Planarity : 0.004 0.061 3436 Dihedral : 5.725 34.809 3428 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.95 % Favored : 94.80 % Rotamer: Outliers : 2.54 % Allowed : 14.74 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.17), residues: 2444 helix: -1.03 (1.06), residues: 24 sheet: -0.25 (0.17), residues: 948 loop : -1.27 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.009 0.001 TYR D 121 PHE 0.011 0.001 PHE C 354 TRP 0.015 0.001 TRP C 178 HIS 0.003 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00271 (19980) covalent geometry : angle 0.51857 (27108) SS BOND : bond 0.00169 ( 44) SS BOND : angle 1.33310 ( 88) hydrogen bonds : bond 0.03260 ( 566) hydrogen bonds : angle 6.39307 ( 1653) Misc. bond : bond 0.00029 ( 4) link_ALPHA1-3 : bond 0.01057 ( 4) link_ALPHA1-3 : angle 1.36280 ( 12) link_ALPHA1-6 : bond 0.00955 ( 4) link_ALPHA1-6 : angle 2.63136 ( 12) link_BETA1-4 : bond 0.00586 ( 8) link_BETA1-4 : angle 1.22096 ( 24) link_NAG-ASN : bond 0.00537 ( 20) link_NAG-ASN : angle 3.42381 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 CYS cc_start: 0.6733 (m) cc_final: 0.6075 (m) REVERT: A 325 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.7985 (m) REVERT: H 38 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7137 (ptp-170) REVERT: L 13 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6280 (ppp) REVERT: L 61 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7260 (ttp80) REVERT: E 38 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7135 (ptp-170) REVERT: I 13 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6332 (ppp) REVERT: I 61 ARG cc_start: 0.7530 (ttp-170) cc_final: 0.7258 (ttp80) REVERT: C 294 ASN cc_start: 0.8493 (t0) cc_final: 0.8083 (t0) REVERT: C 318 CYS cc_start: 0.6721 (m) cc_final: 0.6095 (m) REVERT: C 325 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.7991 (m) REVERT: F 38 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7123 (ptp-170) REVERT: J 61 ARG cc_start: 0.7521 (ttp-170) cc_final: 0.7176 (ttp80) REVERT: D 292 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7953 (ttm170) REVERT: D 293 ASP cc_start: 0.8080 (t70) cc_final: 0.7792 (t70) REVERT: D 318 CYS cc_start: 0.6639 (m) cc_final: 0.5988 (m) REVERT: G 38 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7134 (ptp-170) REVERT: K 13 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6315 (ppp) REVERT: K 61 ARG cc_start: 0.7578 (ttp80) cc_final: 0.7289 (ttp80) outliers start: 54 outliers final: 34 residues processed: 264 average time/residue: 0.1179 time to fit residues: 49.9290 Evaluate side-chains 265 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain K residue 13 MET Chi-restraints excluded: chain K residue 72 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 152 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 115 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 208 optimal weight: 5.9990 chunk 209 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 233 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.140664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.113687 restraints weight = 20991.500| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.67 r_work: 0.3056 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20064 Z= 0.119 Angle : 0.542 8.795 27304 Z= 0.276 Chirality : 0.044 0.185 3028 Planarity : 0.003 0.061 3436 Dihedral : 5.616 33.733 3428 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.95 % Favored : 94.80 % Rotamer: Outliers : 3.01 % Allowed : 14.41 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.17), residues: 2444 helix: -0.88 (1.06), residues: 24 sheet: -0.19 (0.17), residues: 948 loop : -1.22 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 156 TYR 0.009 0.001 TYR B 121 PHE 0.011 0.001 PHE C 354 TRP 0.015 0.001 TRP C 178 HIS 0.002 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00272 (19980) covalent geometry : angle 0.51273 (27108) SS BOND : bond 0.00200 ( 44) SS BOND : angle 1.66509 ( 88) hydrogen bonds : bond 0.03226 ( 566) hydrogen bonds : angle 6.29247 ( 1653) Misc. bond : bond 0.00024 ( 4) link_ALPHA1-3 : bond 0.01048 ( 4) link_ALPHA1-3 : angle 1.36772 ( 12) link_ALPHA1-6 : bond 0.00936 ( 4) link_ALPHA1-6 : angle 2.57976 ( 12) link_BETA1-4 : bond 0.00555 ( 8) link_BETA1-4 : angle 1.17885 ( 24) link_NAG-ASN : bond 0.00471 ( 20) link_NAG-ASN : angle 2.94841 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 235 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 CYS cc_start: 0.6744 (m) cc_final: 0.6122 (m) REVERT: A 325 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.8001 (m) REVERT: H 38 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7188 (ptp-170) REVERT: L 13 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6336 (ppp) REVERT: L 61 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7382 (ttp80) REVERT: B 390 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8232 (mp) REVERT: E 38 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7184 (ptp-170) REVERT: I 13 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6413 (ppp) REVERT: I 61 ARG cc_start: 0.7605 (ttp-170) cc_final: 0.7342 (ttp80) REVERT: C 294 ASN cc_start: 0.8505 (t0) cc_final: 0.8090 (t0) REVERT: C 318 CYS cc_start: 0.6692 (m) cc_final: 0.6106 (m) REVERT: C 325 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.8010 (m) REVERT: C 380 ILE cc_start: 0.9091 (mm) cc_final: 0.8872 (mt) REVERT: F 38 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7185 (ptp-170) REVERT: J 61 ARG cc_start: 0.7597 (ttp-170) cc_final: 0.7339 (ttp80) REVERT: D 292 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7999 (ttm170) REVERT: D 293 ASP cc_start: 0.8112 (t70) cc_final: 0.7865 (t70) REVERT: D 318 CYS cc_start: 0.6669 (m) cc_final: 0.6055 (m) REVERT: D 325 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8122 (m) REVERT: G 38 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7195 (ptp-170) REVERT: K 13 MET cc_start: 0.7099 (OUTLIER) cc_final: 0.6375 (ppp) REVERT: K 61 ARG cc_start: 0.7658 (ttp80) cc_final: 0.7384 (ttp80) outliers start: 64 outliers final: 46 residues processed: 275 average time/residue: 0.1290 time to fit residues: 57.8418 Evaluate side-chains 288 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 230 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain K residue 13 MET Chi-restraints excluded: chain K residue 72 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 139 optimal weight: 0.2980 chunk 163 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.119569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.096956 restraints weight = 22140.245| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.26 r_work: 0.2963 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20064 Z= 0.207 Angle : 0.630 9.878 27304 Z= 0.319 Chirality : 0.046 0.203 3028 Planarity : 0.004 0.061 3436 Dihedral : 6.150 38.502 3428 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % Rotamer: Outliers : 2.87 % Allowed : 14.60 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.17), residues: 2444 helix: -1.00 (1.11), residues: 24 sheet: -0.35 (0.17), residues: 996 loop : -1.29 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 156 TYR 0.014 0.001 TYR D 121 PHE 0.017 0.002 PHE D 132 TRP 0.012 0.002 TRP B 178 HIS 0.007 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00495 (19980) covalent geometry : angle 0.58649 (27108) SS BOND : bond 0.00354 ( 44) SS BOND : angle 2.32918 ( 88) hydrogen bonds : bond 0.03633 ( 566) hydrogen bonds : angle 6.62015 ( 1653) Misc. bond : bond 0.00039 ( 4) link_ALPHA1-3 : bond 0.01002 ( 4) link_ALPHA1-3 : angle 1.59216 ( 12) link_ALPHA1-6 : bond 0.00747 ( 4) link_ALPHA1-6 : angle 2.22680 ( 12) link_BETA1-4 : bond 0.00497 ( 8) link_BETA1-4 : angle 1.32605 ( 24) link_NAG-ASN : bond 0.00446 ( 20) link_NAG-ASN : angle 3.89324 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4888 Ramachandran restraints generated. 2444 Oldfield, 0 Emsley, 2444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 239 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8142 (m) REVERT: A 407 SER cc_start: 0.9173 (p) cc_final: 0.8847 (t) REVERT: H 38 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7269 (ptp-170) REVERT: L 13 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6320 (ppp) REVERT: L 61 ARG cc_start: 0.7748 (ttp80) cc_final: 0.7486 (ttp80) REVERT: E 38 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7252 (ptp-170) REVERT: I 13 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6374 (ppp) REVERT: I 61 ARG cc_start: 0.7717 (ttp-170) cc_final: 0.7436 (ttp80) REVERT: C 294 ASN cc_start: 0.8775 (t0) cc_final: 0.8244 (t0) REVERT: C 325 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8111 (m) REVERT: F 38 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7265 (ptp-170) REVERT: J 61 ARG cc_start: 0.7705 (ttp-170) cc_final: 0.7426 (ttp80) REVERT: D 292 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7709 (ttm170) REVERT: D 325 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8197 (m) REVERT: D 407 SER cc_start: 0.9180 (p) cc_final: 0.8855 (t) REVERT: G 38 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7237 (ptp-170) REVERT: K 13 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6369 (ppp) REVERT: K 61 ARG cc_start: 0.7771 (ttp80) cc_final: 0.7497 (ttp80) outliers start: 61 outliers final: 46 residues processed: 274 average time/residue: 0.1361 time to fit residues: 60.1756 Evaluate side-chains 293 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 236 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 271 SER Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain F residue 38 ARG Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 107 THR Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 183 CYS Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain K residue 13 MET Chi-restraints excluded: chain K residue 72 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 239 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 132 optimal weight: 0.4980 chunk 209 optimal weight: 0.6980 chunk 206 optimal weight: 0.9980 chunk 73 optimal weight: 0.0570 chunk 138 optimal weight: 2.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 ASN C 173 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.141624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.120090 restraints weight = 21087.405| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.40 r_work: 0.2935 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20064 Z= 0.117 Angle : 0.557 9.026 27304 Z= 0.283 Chirality : 0.044 0.185 3028 Planarity : 0.003 0.062 3436 Dihedral : 5.680 33.512 3428 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.46 % Favored : 95.29 % Rotamer: Outliers : 2.31 % Allowed : 15.35 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.17), residues: 2444 helix: -0.91 (1.05), residues: 24 sheet: -0.22 (0.17), residues: 944 loop : -1.17 (0.16), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 292 TYR 0.010 0.001 TYR B 121 PHE 0.011 0.001 PHE C 354 TRP 0.017 0.001 TRP C 178 HIS 0.007 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00266 (19980) covalent geometry : angle 0.52316 (27108) SS BOND : bond 0.00215 ( 44) SS BOND : angle 1.83867 ( 88) hydrogen bonds : bond 0.03220 ( 566) hydrogen bonds : angle 6.35759 ( 1653) Misc. bond : bond 0.00034 ( 4) link_ALPHA1-3 : bond 0.01094 ( 4) link_ALPHA1-3 : angle 1.33752 ( 12) link_ALPHA1-6 : bond 0.00901 ( 4) link_ALPHA1-6 : angle 2.70028 ( 12) link_BETA1-4 : bond 0.00507 ( 8) link_BETA1-4 : angle 1.22590 ( 24) link_NAG-ASN : bond 0.00389 ( 20) link_NAG-ASN : angle 3.21996 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4290.72 seconds wall clock time: 74 minutes 47.50 seconds (4487.50 seconds total)