Starting phenix.real_space_refine on Sat Jul 4 09:34:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9md2_48165/07_2026/9md2_48165.cif Found real_map, /net/cci-nas-00/data/ceres_data/9md2_48165/07_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_48165/07_2026/9md2_48165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9md2_48165/07_2026/9md2_48165.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9md2_48165/07_2026/9md2_48165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9md2_48165/07_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-dev-6108/lib/python3.11/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, 56 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 1 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, 56 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 1 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, 56 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 1 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, 56 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 2} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.35, per 1000 atoms: 0.22 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: 1.86 Conformation dependent library (CDL) restraints added in 801.8 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: 0.72 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: 3.84 Time building geometry restraints manager: 2.41 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: 2.960 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 19.030 Find NCS groups from input model: 0.370 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: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 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/Z covalent geometry : bond 0.00247 / 0.11 (19980) covalent geometry : angle 0.55001 / 0.28 (27108) SS BOND : bond 0.00198 / 0.12 ( 44) SS BOND : angle 1.32926 / 1.00 ( 88) hydrogen bonds : bond 0.25124 / 16.92 ( 566) hydrogen bonds : angle 11.67659 / 8.26 ( 1653) Misc. bond : bond 0.00037 / 0.02 ( 4) link_ALPHA1-3 : bond 0.01060 / 0.62 ( 4) link_ALPHA1-3 : angle 1.51253 / 0.75 ( 12) link_ALPHA1-6 : bond 0.01037 / 0.61 ( 4) link_ALPHA1-6 : angle 2.52728 / 1.27 ( 12) link_BETA1-4 : bond 0.00497 / 0.33 ( 8) link_BETA1-4 : angle 1.23636 / 0.76 ( 24) link_NAG-ASN : bond 0.00277 / 0.17 ( 20) link_NAG-ASN : angle 3.44003 / 2.22 ( 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 : 0.776 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: 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: 0.1287 time to fit residues: 59.7136 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 : 0.731 ------------------------------------------------------------------------------- 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... ** 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 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 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.133986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.107132 restraints weight = 21353.758| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.53 r_work: 0.3113 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20064 Z= 0.150 Angle : 0.598 7.030 27304 Z= 0.310 Chirality : 0.045 0.188 3028 Planarity : 0.005 0.055 3436 Dihedral : 6.161 43.820 3428 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.52 % Favored : 94.31 % Rotamer: Outliers : 0.47 % Allowed : 8.47 % Favored : 91.05 % 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: -1.46 (0.16), residues: 2444 helix: -2.40 (0.85), residues: 24 sheet: -0.14 (0.18), residues: 912 loop : -1.54 (0.15), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 172 TYR 0.017 0.001 TYR B 155 PHE 0.013 0.002 PHE D 132 TRP 0.020 0.001 TRP F 100C HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (19980) covalent geometry : angle 0.57757 / 0.31 (27108) SS BOND : bond 0.00266 / 0.16 ( 44) SS BOND : angle 1.06786 / 0.80 ( 88) hydrogen bonds : bond 0.04464 / 3.01 ( 566) hydrogen bonds : angle 8.28935 / 5.80 ( 1653) Misc. bond : bond 0.00020 / 0.01 ( 4) link_ALPHA1-3 : bond 0.01057 / 0.63 ( 4) link_ALPHA1-3 : angle 1.41778 / 0.70 ( 12) link_ALPHA1-6 : bond 0.00958 / 0.57 ( 4) link_ALPHA1-6 : angle 2.66380 / 1.33 ( 12) link_BETA1-4 : bond 0.00558 / 0.36 ( 8) link_BETA1-4 : angle 1.25165 / 0.74 ( 24) link_NAG-ASN : bond 0.00294 / 0.17 ( 20) link_NAG-ASN : angle 2.85493 / 1.82 ( 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 277 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 267 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: L 61 ARG cc_start: 0.7399 (ttp80) cc_final: 0.7159 (ttp80) REVERT: B 293 ASP cc_start: 0.8267 (t70) cc_final: 0.7983 (t70) REVERT: I 61 ARG cc_start: 0.7397 (ttp80) cc_final: 0.7061 (ttp80) REVERT: C 86 ASN cc_start: 0.8438 (m-40) cc_final: 0.8175 (m-40) REVERT: J 61 ARG cc_start: 0.7511 (ttp-170) cc_final: 0.7248 (ttp80) REVERT: K 61 ARG cc_start: 0.7408 (ttp80) cc_final: 0.7176 (ttp80) outliers start: 10 outliers final: 10 residues processed: 270 average time/residue: 0.1280 time to fit residues: 56.9847 Evaluate side-chains 254 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 244 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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 D residue 95 THR 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: 3.9990 chunk 133 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 chunk 111 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 153 optimal weight: 0.0980 chunk 158 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 HIS ** 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 = 0.3442 r_free = 0.3442 target = 0.136796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.109128 restraints weight = 21302.755| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.66 r_work: 0.2859 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20064 Z= 0.141 Angle : 0.569 7.147 27304 Z= 0.290 Chirality : 0.045 0.189 3028 Planarity : 0.004 0.054 3436 Dihedral : 5.878 35.985 3428 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.68 % Favored : 96.15 % Rotamer: Outliers : 1.55 % Allowed : 10.92 % Favored : 87.52 % 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: -1.45 (0.17), residues: 2444 helix: -1.71 (0.99), residues: 24 sheet: -0.24 (0.18), residues: 924 loop : -1.46 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 156 TYR 0.013 0.001 TYR B 155 PHE 0.011 0.001 PHE C 354 TRP 0.018 0.001 TRP C 178 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (19980) covalent geometry : angle 0.54458 / 0.29 (27108) SS BOND : bond 0.00194 / 0.12 ( 44) SS BOND : angle 1.09624 / 0.84 ( 88) hydrogen bonds : bond 0.04100 / 2.76 ( 566) hydrogen bonds : angle 7.42993 / 5.17 ( 1653) Misc. bond : bond 0.00025 / 0.01 ( 4) link_ALPHA1-3 : bond 0.01045 / 0.62 ( 4) link_ALPHA1-3 : angle 1.43824 / 0.71 ( 12) link_ALPHA1-6 : bond 0.00879 / 0.52 ( 4) link_ALPHA1-6 : angle 2.58379 / 1.29 ( 12) link_BETA1-4 : bond 0.00502 / 0.33 ( 8) link_BETA1-4 : angle 1.25604 / 0.76 ( 24) link_NAG-ASN : bond 0.00394 / 0.24 ( 20) link_NAG-ASN : angle 3.03141 / 1.94 ( 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 288 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 255 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 13 MET cc_start: 0.6927 (ppp) cc_final: 0.6416 (ppp) REVERT: L 61 ARG cc_start: 0.7420 (ttp80) cc_final: 0.7158 (ttp80) REVERT: B 86 ASN cc_start: 0.8486 (m-40) cc_final: 0.8248 (m-40) REVERT: I 13 MET cc_start: 0.6974 (ppp) cc_final: 0.6357 (ppp) REVERT: I 21 ILE cc_start: 0.7268 (mt) cc_final: 0.7060 (tt) REVERT: I 61 ARG cc_start: 0.7412 (ttp80) cc_final: 0.7070 (ttp80) REVERT: C 86 ASN cc_start: 0.8489 (m-40) cc_final: 0.8231 (m-40) REVERT: J 21 ILE cc_start: 0.7227 (mt) cc_final: 0.7014 (tt) REVERT: J 61 ARG cc_start: 0.7499 (ttp-170) cc_final: 0.7188 (ttp80) REVERT: D 86 ASN cc_start: 0.8507 (m-40) cc_final: 0.8251 (m-40) REVERT: K 13 MET cc_start: 0.6953 (ppp) cc_final: 0.6448 (ppp) REVERT: K 21 ILE cc_start: 0.7239 (mt) cc_final: 0.7032 (tt) REVERT: K 61 ARG cc_start: 0.7439 (ttp80) cc_final: 0.7175 (ttp80) outliers start: 33 outliers final: 33 residues processed: 267 average time/residue: 0.1291 time to fit residues: 56.9529 Evaluate side-chains 270 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 237 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 2.9990 chunk 57 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.150348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.127498 restraints weight = 20527.356| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.50 r_work: 0.3031 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20064 Z= 0.120 Angle : 0.535 7.136 27304 Z= 0.272 Chirality : 0.044 0.185 3028 Planarity : 0.004 0.057 3436 Dihedral : 5.658 34.428 3428 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.97 % Rotamer: Outliers : 2.02 % Allowed : 12.29 % Favored : 85.69 % 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: -1.31 (0.17), residues: 2444 helix: -1.33 (1.03), residues: 24 sheet: -0.25 (0.17), residues: 960 loop : -1.31 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 156 TYR 0.010 0.001 TYR B 121 PHE 0.011 0.001 PHE C 354 TRP 0.019 0.001 TRP C 178 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (19980) covalent geometry : angle 0.51264 / 0.27 (27108) SS BOND : bond 0.00162 / 0.10 ( 44) SS BOND : angle 1.05046 / 0.80 ( 88) hydrogen bonds : bond 0.03556 / 2.39 ( 566) hydrogen bonds : angle 6.87346 / 4.76 ( 1653) Misc. bond : bond 0.00025 / 0.01 ( 4) link_ALPHA1-3 : bond 0.01061 / 0.63 ( 4) link_ALPHA1-3 : angle 1.36133 / 0.68 ( 12) link_ALPHA1-6 : bond 0.00908 / 0.53 ( 4) link_ALPHA1-6 : angle 2.64083 / 1.32 ( 12) link_BETA1-4 : bond 0.00544 / 0.36 ( 8) link_BETA1-4 : angle 1.17027 / 0.71 ( 24) link_NAG-ASN : bond 0.00288 / 0.16 ( 20) link_NAG-ASN : angle 2.71234 / 1.78 ( 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 290 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.8201 (ttt180) REVERT: L 13 MET cc_start: 0.6865 (ppp) cc_final: 0.6326 (ppp) REVERT: L 21 ILE cc_start: 0.6575 (OUTLIER) cc_final: 0.6306 (tt) REVERT: L 61 ARG cc_start: 0.7570 (ttp80) cc_final: 0.7316 (ttp80) REVERT: B 463 ASP cc_start: 0.8259 (m-30) cc_final: 0.8044 (m-30) REVERT: I 13 MET cc_start: 0.6948 (ppp) cc_final: 0.6279 (ppp) REVERT: I 61 ARG cc_start: 0.7591 (ttp80) cc_final: 0.7277 (ttp80) REVERT: C 86 ASN cc_start: 0.8596 (m-40) cc_final: 0.8378 (m-40) REVERT: J 61 ARG cc_start: 0.7555 (ttp-170) cc_final: 0.7325 (ttp80) REVERT: D 86 ASN cc_start: 0.8605 (m-40) cc_final: 0.8387 (m-40) REVERT: K 13 MET cc_start: 0.6922 (ppp) cc_final: 0.6362 (ppp) REVERT: K 61 ARG cc_start: 0.7598 (ttp80) cc_final: 0.7335 (ttp80) outliers start: 43 outliers final: 31 residues processed: 268 average time/residue: 0.1277 time to fit residues: 56.6401 Evaluate side-chains 267 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 369 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain H residue 100 TRP Chi-restraints excluded: chain L residue 21 ILE 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 B residue 369 THR Chi-restraints excluded: chain E residue 100 TRP Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 109 SER 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 J residue 72 VAL 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 338 LEU Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 443 ILE 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: 2.9990 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 206 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 233 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 184 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.139868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.111931 restraints weight = 21157.441| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.74 r_work: 0.3004 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20064 Z= 0.120 Angle : 0.529 6.674 27304 Z= 0.268 Chirality : 0.044 0.182 3028 Planarity : 0.004 0.057 3436 Dihedral : 5.568 34.828 3428 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.13 % Favored : 95.70 % Rotamer: Outliers : 2.73 % Allowed : 12.29 % Favored : 84.98 % 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: -1.23 (0.17), residues: 2444 helix: -1.09 (1.04), residues: 24 sheet: -0.19 (0.17), residues: 960 loop : -1.26 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 156 TYR 0.010 0.001 TYR B 121 PHE 0.011 0.001 PHE C 354 TRP 0.015 0.001 TRP C 178 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (19980) covalent geometry : angle 0.50727 / 0.26 (27108) SS BOND : bond 0.00185 / 0.11 ( 44) SS BOND : angle 1.07394 / 0.82 ( 88) hydrogen bonds : bond 0.03415 / 2.30 ( 566) hydrogen bonds : angle 6.62402 / 4.58 ( 1653) Misc. bond : bond 0.00020 / 0.01 ( 4) link_ALPHA1-3 : bond 0.01062 / 0.62 ( 4) link_ALPHA1-3 : angle 1.41610 / 0.71 ( 12) link_ALPHA1-6 : bond 0.00875 / 0.51 ( 4) link_ALPHA1-6 : angle 2.54494 / 1.27 ( 12) link_BETA1-4 : bond 0.00547 / 0.36 ( 8) link_BETA1-4 : angle 1.17237 / 0.71 ( 24) link_NAG-ASN : bond 0.00216 / 0.13 ( 20) link_NAG-ASN : angle 2.66232 / 1.76 ( 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 302 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.8103 (ttt180) REVERT: H 38 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7217 (ptp-170) REVERT: L 13 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6193 (ppp) REVERT: L 21 ILE cc_start: 0.6328 (OUTLIER) cc_final: 0.6067 (tt) REVERT: L 61 ARG cc_start: 0.7506 (ttp80) cc_final: 0.7237 (ttp80) REVERT: E 38 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7158 (ptp-170) REVERT: I 13 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6193 (ppp) REVERT: I 61 ARG cc_start: 0.7516 (ttp80) cc_final: 0.7182 (ttp80) REVERT: C 86 ASN cc_start: 0.8486 (m-40) cc_final: 0.8244 (m-40) REVERT: C 294 ASN cc_start: 0.8386 (t0) cc_final: 0.7933 (t0) REVERT: F 38 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7201 (ptp-170) REVERT: J 61 ARG cc_start: 0.7471 (ttp-170) cc_final: 0.7193 (ttp80) REVERT: D 86 ASN cc_start: 0.8488 (m-40) cc_final: 0.8243 (m-40) REVERT: D 103 ASP cc_start: 0.8193 (t70) cc_final: 0.7937 (t70) REVERT: G 38 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7207 (ptp-170) REVERT: K 13 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6221 (ppp) REVERT: K 61 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7218 (ttp80) outliers start: 58 outliers final: 41 residues processed: 274 average time/residue: 0.1239 time to fit residues: 55.0125 Evaluate side-chains 281 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 232 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 338 LEU Chi-restraints excluded: chain A residue 369 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 L residue 13 MET Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 109 SER 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 338 LEU Chi-restraints excluded: chain B residue 369 THR 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 109 SER 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 380 ILE 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 109 SER 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 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: 4.9990 chunk 153 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 151 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 184 HIS D 441 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.121575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.100010 restraints weight = 21788.547| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.28 r_work: 0.2892 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20064 Z= 0.189 Angle : 0.586 6.106 27304 Z= 0.299 Chirality : 0.045 0.199 3028 Planarity : 0.004 0.056 3436 Dihedral : 5.966 37.368 3428 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 2.87 % Allowed : 12.95 % Favored : 84.18 % 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: -1.31 (0.17), residues: 2444 helix: -1.10 (1.05), residues: 24 sheet: -0.24 (0.17), residues: 952 loop : -1.33 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 156 TYR 0.015 0.001 TYR C 121 PHE 0.017 0.002 PHE C 410 TRP 0.014 0.001 TRP F 100C HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (19980) covalent geometry : angle 0.56105 / 0.29 (27108) SS BOND : bond 0.00285 / 0.17 ( 44) SS BOND : angle 1.35511 / 1.01 ( 88) hydrogen bonds : bond 0.03653 / 2.45 ( 566) hydrogen bonds : angle 6.66548 / 4.61 ( 1653) Misc. bond : bond 0.00038 / 0.02 ( 4) link_ALPHA1-3 : bond 0.01025 / 0.60 ( 4) link_ALPHA1-3 : angle 1.58610 / 0.78 ( 12) link_ALPHA1-6 : bond 0.00777 / 0.46 ( 4) link_ALPHA1-6 : angle 2.25999 / 1.14 ( 12) link_BETA1-4 : bond 0.00475 / 0.30 ( 8) link_BETA1-4 : angle 1.28392 / 0.75 ( 24) link_NAG-ASN : bond 0.00378 / 0.23 ( 20) link_NAG-ASN : angle 3.02694 / 1.97 ( 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 306 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 245 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 293 ASP cc_start: 0.8007 (t70) cc_final: 0.7789 (t70) REVERT: H 38 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7262 (ptp-170) REVERT: L 13 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6184 (ppp) REVERT: L 21 ILE cc_start: 0.6550 (OUTLIER) cc_final: 0.6273 (tt) REVERT: L 61 ARG cc_start: 0.7631 (ttp80) cc_final: 0.7333 (ttp80) REVERT: E 38 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7220 (ptp-170) REVERT: I 13 MET cc_start: 0.6993 (OUTLIER) cc_final: 0.6214 (ppp) REVERT: I 61 ARG cc_start: 0.7668 (ttp80) cc_final: 0.7127 (ttp80) REVERT: C 293 ASP cc_start: 0.8121 (t70) cc_final: 0.7905 (t70) REVERT: F 38 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7272 (ptp-170) REVERT: J 61 ARG cc_start: 0.7594 (ttp-170) cc_final: 0.7304 (ttp80) REVERT: D 86 ASN cc_start: 0.8535 (m-40) cc_final: 0.8312 (m-40) REVERT: D 103 ASP cc_start: 0.8231 (t70) cc_final: 0.7966 (t70) REVERT: D 293 ASP cc_start: 0.8018 (t70) cc_final: 0.7781 (t70) REVERT: G 38 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.7258 (ptp-170) REVERT: K 13 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6226 (ppp) REVERT: K 61 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7317 (ttp80) outliers start: 61 outliers final: 44 residues processed: 278 average time/residue: 0.1165 time to fit residues: 52.4962 Evaluate side-chains 289 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 237 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 443 ILE 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 L residue 13 MET Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 109 SER 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 369 THR Chi-restraints excluded: chain B residue 379 VAL 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 100 TRP 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 109 SER 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 C residue 369 THR 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 109 SER 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 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 38 ARG Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 100 TRP 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: 0.4980 chunk 102 optimal weight: 0.0170 chunk 5 optimal weight: 0.7980 chunk 235 optimal weight: 10.0000 chunk 145 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN ** 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 = 0.3607 r_free = 0.3607 target = 0.149770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.128792 restraints weight = 20559.986| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.52 r_work: 0.2981 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 20064 Z= 0.112 Angle : 0.528 6.182 27304 Z= 0.269 Chirality : 0.044 0.185 3028 Planarity : 0.004 0.059 3436 Dihedral : 5.588 33.634 3428 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.46 % Favored : 95.38 % Rotamer: Outliers : 2.21 % Allowed : 14.03 % Favored : 83.76 % 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: -1.20 (0.17), residues: 2444 helix: -1.01 (0.98), residues: 24 sheet: -0.20 (0.17), residues: 960 loop : -1.23 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 156 TYR 0.009 0.001 TYR C 121 PHE 0.011 0.001 PHE C 354 TRP 0.016 0.001 TRP C 178 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (19980) covalent geometry : angle 0.50500 / 0.26 (27108) SS BOND : bond 0.00171 / 0.10 ( 44) SS BOND : angle 1.20287 / 0.89 ( 88) hydrogen bonds : bond 0.03272 / 2.20 ( 566) hydrogen bonds : angle 6.38896 / 4.42 ( 1653) Misc. bond : bond 0.00024 / 0.01 ( 4) link_ALPHA1-3 : bond 0.01091 / 0.64 ( 4) link_ALPHA1-3 : angle 1.37401 / 0.69 ( 12) link_ALPHA1-6 : bond 0.00914 / 0.54 ( 4) link_ALPHA1-6 : angle 2.66356 / 1.33 ( 12) link_BETA1-4 : bond 0.00509 / 0.35 ( 8) link_BETA1-4 : angle 1.19975 / 0.73 ( 24) link_NAG-ASN : bond 0.00396 / 0.21 ( 20) link_NAG-ASN : angle 2.66352 / 1.74 ( 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 285 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 238 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 CYS cc_start: 0.6982 (m) cc_final: 0.6371 (m) REVERT: H 38 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7388 (ptp-170) REVERT: L 13 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6262 (ppp) REVERT: L 21 ILE cc_start: 0.6472 (OUTLIER) cc_final: 0.6215 (tt) REVERT: L 61 ARG cc_start: 0.7735 (ttp80) cc_final: 0.7324 (ttp80) REVERT: E 38 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7379 (ptp-170) REVERT: I 13 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6222 (ppp) REVERT: I 61 ARG cc_start: 0.7746 (ttp80) cc_final: 0.7440 (ttp80) REVERT: C 294 ASN cc_start: 0.8493 (t0) cc_final: 0.8033 (t0) REVERT: F 38 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7393 (ptp-170) REVERT: J 61 ARG cc_start: 0.7650 (ttp-170) cc_final: 0.7373 (ttp80) REVERT: D 103 ASP cc_start: 0.8322 (t0) cc_final: 0.8029 (t0) REVERT: D 293 ASP cc_start: 0.8097 (t70) cc_final: 0.7854 (t70) REVERT: D 318 CYS cc_start: 0.6854 (m) cc_final: 0.6236 (m) REVERT: G 38 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7421 (ptp-170) REVERT: K 13 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6316 (ppp) REVERT: K 61 ARG cc_start: 0.7723 (ttp80) cc_final: 0.7441 (ttp80) outliers start: 47 outliers final: 29 residues processed: 271 average time/residue: 0.1288 time to fit residues: 56.7418 Evaluate side-chains 266 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 229 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 443 ILE 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 21 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 183 CYS Chi-restraints excluded: chain B residue 230 CYS 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 C residue 95 THR Chi-restraints excluded: chain C residue 109 SER 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 J residue 72 VAL Chi-restraints excluded: chain D residue 109 SER 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 114 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 86 optimal weight: 0.1980 chunk 132 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 226 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 = 0.3422 r_free = 0.3422 target = 0.134738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.106432 restraints weight = 21394.398| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.81 r_work: 0.2781 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20064 Z= 0.169 Angle : 0.570 5.981 27304 Z= 0.290 Chirality : 0.045 0.193 3028 Planarity : 0.004 0.058 3436 Dihedral : 5.865 36.157 3428 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.48 % Favored : 94.35 % Rotamer: Outliers : 2.64 % Allowed : 13.98 % Favored : 83.38 % 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: -1.24 (0.17), residues: 2444 helix: -0.90 (1.04), residues: 24 sheet: -0.23 (0.17), residues: 960 loop : -1.25 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 156 TYR 0.012 0.001 TYR C 121 PHE 0.013 0.001 PHE D 132 TRP 0.012 0.001 TRP C 178 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (19980) covalent geometry : angle 0.54176 / 0.28 (27108) SS BOND : bond 0.00278 / 0.15 ( 44) SS BOND : angle 1.58803 / 1.17 ( 88) hydrogen bonds : bond 0.03468 / 2.32 ( 566) hydrogen bonds : angle 6.39234 / 4.42 ( 1653) Misc. bond : bond 0.00030 / 0.02 ( 4) link_ALPHA1-3 : bond 0.01038 / 0.61 ( 4) link_ALPHA1-3 : angle 1.50116 / 0.74 ( 12) link_ALPHA1-6 : bond 0.00780 / 0.46 ( 4) link_ALPHA1-6 : angle 2.33637 / 1.18 ( 12) link_BETA1-4 : bond 0.00516 / 0.33 ( 8) link_BETA1-4 : angle 1.26498 / 0.75 ( 24) link_NAG-ASN : bond 0.00882 / 0.46 ( 20) link_NAG-ASN : angle 3.04466 / 2.03 ( 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 294 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 238 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7163 (ptp-170) REVERT: L 13 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6253 (ppp) REVERT: L 21 ILE cc_start: 0.6300 (OUTLIER) cc_final: 0.6033 (tt) REVERT: L 61 ARG cc_start: 0.7534 (ttp80) cc_final: 0.7234 (ttp80) REVERT: E 38 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7130 (ptp-170) REVERT: I 13 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6225 (ppp) REVERT: C 294 ASN cc_start: 0.8551 (t0) cc_final: 0.8036 (t0) REVERT: F 38 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7153 (ptp-170) REVERT: J 61 ARG cc_start: 0.7480 (ttp-170) cc_final: 0.7124 (ttp80) REVERT: D 103 ASP cc_start: 0.8335 (t0) cc_final: 0.8046 (t0) REVERT: D 293 ASP cc_start: 0.8061 (t70) cc_final: 0.7803 (t70) REVERT: D 318 CYS cc_start: 0.6813 (m) cc_final: 0.6154 (m) REVERT: G 38 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7177 (ptp-170) REVERT: K 13 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6331 (ppp) REVERT: K 61 ARG cc_start: 0.7524 (ttp80) cc_final: 0.7197 (ttp80) outliers start: 56 outliers final: 36 residues processed: 275 average time/residue: 0.1317 time to fit residues: 58.7847 Evaluate side-chains 274 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 230 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 443 ILE 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 L residue 13 MET Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 109 SER 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 100 TRP 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 109 SER 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 C residue 380 ILE 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 109 SER 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 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: 1.9990 chunk 212 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 209 optimal weight: 0.7980 chunk 135 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 233 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 226 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 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 = 0.3258 r_free = 0.3258 target = 0.125015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.098771 restraints weight = 21789.392| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.50 r_work: 0.3112 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20064 Z= 0.159 Angle : 0.569 8.450 27304 Z= 0.291 Chirality : 0.045 0.193 3028 Planarity : 0.004 0.058 3436 Dihedral : 5.870 35.796 3428 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.44 % Favored : 94.31 % Rotamer: Outliers : 2.50 % Allowed : 14.22 % Favored : 83.29 % 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: -1.21 (0.17), residues: 2444 helix: -0.89 (1.02), residues: 24 sheet: -0.23 (0.17), residues: 960 loop : -1.22 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 156 TYR 0.012 0.001 TYR C 121 PHE 0.013 0.001 PHE D 132 TRP 0.014 0.001 TRP C 178 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (19980) covalent geometry : angle 0.54104 / 0.28 (27108) SS BOND : bond 0.00291 / 0.15 ( 44) SS BOND : angle 1.73428 / 1.27 ( 88) hydrogen bonds : bond 0.03418 / 2.28 ( 566) hydrogen bonds : angle 6.38917 / 4.42 ( 1653) Misc. bond : bond 0.00033 / 0.02 ( 4) link_ALPHA1-3 : bond 0.01059 / 0.62 ( 4) link_ALPHA1-3 : angle 1.49366 / 0.74 ( 12) link_ALPHA1-6 : bond 0.00797 / 0.47 ( 4) link_ALPHA1-6 : angle 2.41538 / 1.21 ( 12) link_BETA1-4 : bond 0.00471 / 0.30 ( 8) link_BETA1-4 : angle 1.26189 / 0.75 ( 24) link_NAG-ASN : bond 0.00667 / 0.35 ( 20) link_NAG-ASN : angle 2.93709 / 1.91 ( 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 280 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 227 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 38 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7198 (ptp-170) REVERT: L 13 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6292 (ppp) REVERT: L 21 ILE cc_start: 0.6566 (OUTLIER) cc_final: 0.6292 (tt) REVERT: L 61 ARG cc_start: 0.7672 (ttp80) cc_final: 0.7403 (ttp80) REVERT: E 38 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7197 (ptp-170) REVERT: I 13 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6266 (ppp) REVERT: I 61 ARG cc_start: 0.7635 (ttp80) cc_final: 0.7301 (ttp80) REVERT: C 294 ASN cc_start: 0.8564 (t0) cc_final: 0.8063 (t0) REVERT: F 38 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7204 (ptp-170) REVERT: J 61 ARG cc_start: 0.7624 (ttp-170) cc_final: 0.7307 (ttp80) REVERT: D 103 ASP cc_start: 0.8283 (t0) cc_final: 0.8014 (t0) REVERT: D 293 ASP cc_start: 0.7996 (t70) cc_final: 0.7795 (t70) REVERT: D 318 CYS cc_start: 0.6649 (m) cc_final: 0.6010 (m) REVERT: G 38 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7224 (ptp-170) REVERT: K 13 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6388 (ppp) REVERT: K 61 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7394 (ttp80) outliers start: 53 outliers final: 38 residues processed: 261 average time/residue: 0.1189 time to fit residues: 50.6645 Evaluate side-chains 272 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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 443 ILE 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 L residue 13 MET Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 109 SER 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 E residue 100 TRP 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 109 SER 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 C residue 380 ILE 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 109 SER 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 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 30 ASP 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: 8.9990 chunk 125 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 59 optimal weight: 0.0970 chunk 221 optimal weight: 5.9990 chunk 205 optimal weight: 0.4980 chunk 181 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 163 optimal weight: 0.4980 chunk 168 optimal weight: 0.2980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN B 226 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 226 GLN D 226 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.150938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.129700 restraints weight = 20614.517| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.54 r_work: 0.3011 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20064 Z= 0.101 Angle : 0.518 7.800 27304 Z= 0.266 Chirality : 0.043 0.182 3028 Planarity : 0.003 0.060 3436 Dihedral : 5.442 33.417 3428 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.75 % Favored : 95.01 % Rotamer: Outliers : 1.69 % Allowed : 14.97 % Favored : 83.33 % 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: -1.08 (0.17), residues: 2444 helix: -0.61 (1.02), residues: 24 sheet: -0.14 (0.17), residues: 936 loop : -1.12 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 156 TYR 0.008 0.001 TYR B 121 PHE 0.011 0.001 PHE C 354 TRP 0.017 0.001 TRP C 178 HIS 0.005 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (19980) covalent geometry : angle 0.49400 / 0.26 (27108) SS BOND : bond 0.00170 / 0.08 ( 44) SS BOND : angle 1.53115 / 1.11 ( 88) hydrogen bonds : bond 0.03109 / 2.08 ( 566) hydrogen bonds : angle 6.12377 / 4.23 ( 1653) Misc. bond : bond 0.00026 / 0.02 ( 4) link_ALPHA1-3 : bond 0.01073 / 0.63 ( 4) link_ALPHA1-3 : angle 1.24543 / 0.63 ( 12) link_ALPHA1-6 : bond 0.00975 / 0.57 ( 4) link_ALPHA1-6 : angle 2.64688 / 1.32 ( 12) link_BETA1-4 : bond 0.00608 / 0.41 ( 8) link_BETA1-4 : angle 1.13544 / 0.70 ( 24) link_NAG-ASN : bond 0.00504 / 0.26 ( 20) link_NAG-ASN : angle 2.49475 / 1.64 ( 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 269 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 ASN cc_start: 0.8376 (t0) cc_final: 0.7853 (t0) REVERT: H 38 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.7174 (ptp-170) REVERT: L 13 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6349 (ppp) REVERT: L 21 ILE cc_start: 0.6569 (OUTLIER) cc_final: 0.6340 (tt) REVERT: L 61 ARG cc_start: 0.7692 (ttp80) cc_final: 0.7349 (ttp80) REVERT: E 38 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7154 (ptp-170) REVERT: I 13 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6373 (ppp) REVERT: I 61 ARG cc_start: 0.7667 (ttp80) cc_final: 0.7411 (ttp80) REVERT: C 294 ASN cc_start: 0.8413 (t0) cc_final: 0.8015 (t0) REVERT: C 380 ILE cc_start: 0.9046 (mm) cc_final: 0.8808 (mt) REVERT: F 38 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7173 (ptp-170) REVERT: J 50 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7887 (mt-10) REVERT: J 61 ARG cc_start: 0.7636 (ttp-170) cc_final: 0.7380 (ttp80) REVERT: D 103 ASP cc_start: 0.8197 (t0) cc_final: 0.7952 (t0) REVERT: D 318 CYS cc_start: 0.6490 (m) cc_final: 0.5925 (m) REVERT: G 38 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7193 (ptp-170) REVERT: K 13 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6400 (ppp) REVERT: K 61 ARG cc_start: 0.7696 (ttp80) cc_final: 0.7333 (ttp80) outliers start: 36 outliers final: 24 residues processed: 257 average time/residue: 0.1189 time to fit residues: 49.4968 Evaluate side-chains 258 residues out of total 2124 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 443 ILE Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain B residue 109 SER 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 107 THR Chi-restraints excluded: chain I residue 13 MET 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 F residue 38 ARG Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 109 SER 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 338 LEU Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain K residue 13 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 239 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 232 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 132 optimal weight: 0.4980 chunk 209 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 HIS B 199 ASN B 226 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 184 HIS C 226 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 34 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.124317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.097839 restraints weight = 22037.762| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.53 r_work: 0.3079 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.2271 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= 0.204 Angle : 0.604 7.277 27304 Z= 0.310 Chirality : 0.046 0.195 3028 Planarity : 0.004 0.058 3436 Dihedral : 6.051 37.701 3428 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.69 % Favored : 94.07 % Rotamer: Outliers : 2.12 % Allowed : 14.60 % Favored : 83.29 % 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: -1.17 (0.17), residues: 2444 helix: -0.84 (1.07), residues: 24 sheet: -0.14 (0.17), residues: 944 loop : -1.24 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 172 TYR 0.014 0.001 TYR D 121 PHE 0.018 0.002 PHE D 132 TRP 0.012 0.002 TRP A 352 HIS 0.003 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.20 (19980) covalent geometry : angle 0.57388 / 0.30 (27108) SS BOND : bond 0.00361 / 0.20 ( 44) SS BOND : angle 1.97466 / 1.51 ( 88) hydrogen bonds : bond 0.03611 / 2.41 ( 566) hydrogen bonds : angle 6.42288 / 4.44 ( 1653) Misc. bond : bond 0.00024 / 0.01 ( 4) link_ALPHA1-3 : bond 0.01001 / 0.59 ( 4) link_ALPHA1-3 : angle 1.63029 / 0.80 ( 12) link_ALPHA1-6 : bond 0.00743 / 0.44 ( 4) link_ALPHA1-6 : angle 2.15725 / 1.09 ( 12) link_BETA1-4 : bond 0.00516 / 0.33 ( 8) link_BETA1-4 : angle 1.31500 / 0.77 ( 24) link_NAG-ASN : bond 0.00584 / 0.32 ( 20) link_NAG-ASN : angle 3.07067 / 1.97 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4202.22 seconds wall clock time: 73 minutes 25.07 seconds (4405.07 seconds total)