Starting phenix.real_space_refine on Mon Aug 25 20:31:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u72_41966/08_2025/8u72_41966.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u72_41966/08_2025/8u72_41966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u72_41966/08_2025/8u72_41966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u72_41966/08_2025/8u72_41966.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u72_41966/08_2025/8u72_41966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u72_41966/08_2025/8u72_41966.map" } resolution = 3.15 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= 0.025 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1436 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 148 5.49 5 Mg 4 5.21 5 S 74 5.16 5 C 18877 2.51 5 N 5036 2.21 5 O 5573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29712 Number of models: 1 Model: "" Number of chains: 31 Chain: "U" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNA': 19} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "V" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "H" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3143 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 12, 'TRANS': 404} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 359 Unresolved non-hydrogen angles: 441 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 20, 'GLU:plan': 18, 'ARG:plan': 3, 'GLN:plan1': 6, 'ASN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 234 Chain: "I" Number of atoms: 3533 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3529 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 25, 'TRANS': 428} Chain breaks: 1 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 15, 'ASP:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 90 Conformer: "B" Number of residues, atoms: 454, 3529 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 25, 'TRANS': 428} Chain breaks: 1 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 178 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 15, 'ASP:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 90 bond proxies already assigned to first conformer: 3615 Chain: "E" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3452 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 25, 'TRANS': 426} Chain breaks: 1 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 15, 'GLN:plan1': 2, 'ASP:plan': 8, 'ASN:plan1': 4, 'ARG:plan': 3, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 137 Chain: "M" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNA': 19} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "N" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "S" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNA': 19} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "T" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "X" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNA': 19} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "Y" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 3142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3142 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 14, 'TRANS': 396} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 18, 'ASP:plan': 14, 'ARG:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 203 Chain: "B" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3166 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 14, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 336 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 276 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 18, 'ASP:plan': 19, 'ARG:plan': 7, 'PHE:plan': 1, 'GLN:plan1': 6, 'ASN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 234 Chain: "C" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3489 Classifications: {'peptide': 452} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 25, 'TRANS': 426} Chain breaks: 2 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 15, 'ASP:plan': 5, 'ARG:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 108 Chain: "F" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3170 Classifications: {'peptide': 416} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 13, 'TRANS': 402} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 16, 'ASP:plan': 17, 'GLN:plan1': 5, 'ASN:plan1': 7, 'ARG:plan': 4, 'TYR:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 211 Chain: "G" Number of atoms: 3476 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 450, 3468 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 25, 'TRANS': 424} Chain breaks: 3 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 17, 'GLN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 116 Conformer: "B" Number of residues, atoms: 450, 3468 Classifications: {'peptide': 450} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 25, 'TRANS': 424} Chain breaks: 3 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 17, 'GLN:plan1': 1, 'ASP:plan': 4, 'ARG:plan': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 116 bond proxies already assigned to first conformer: 3546 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 8.29, per 1000 atoms: 0.28 Number of scatterers: 29712 At special positions: 0 Unit cell: (126.711, 170.031, 222.015, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 74 16.00 P 148 15.00 Mg 4 11.99 O 5573 8.00 N 5036 7.00 C 18877 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6594 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 39 sheets defined 34.9% alpha, 18.4% beta 36 base pairs and 101 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'H' and resid 15 through 29 Processing helix chain 'H' and resid 44 through 56 removed outlier: 4.068A pdb=" N THR H 48 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE H 49 " --> pdb=" O PHE H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 89 Processing helix chain 'H' and resid 123 through 138 Processing helix chain 'H' and resid 150 through 159 Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 233 through 237 Processing helix chain 'H' and resid 242 through 247 Processing helix chain 'H' and resid 257 through 277 removed outlier: 3.776A pdb=" N ILE H 265 " --> pdb=" O CYS H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 304 removed outlier: 3.919A pdb=" N ASP H 303 " --> pdb=" O LEU H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 365 removed outlier: 3.685A pdb=" N LYS H 363 " --> pdb=" O SER H 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 368 No H-bonds generated for 'chain 'H' and resid 366 through 368' Processing helix chain 'H' and resid 369 through 385 removed outlier: 3.842A pdb=" N LYS H 376 " --> pdb=" O LYS H 372 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU H 384 " --> pdb=" O PHE H 380 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER H 385 " --> pdb=" O ILE H 381 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 17 No H-bonds generated for 'chain 'I' and resid 15 through 17' Processing helix chain 'I' and resid 22 through 30 Processing helix chain 'I' and resid 46 through 60 Processing helix chain 'I' and resid 77 through 83 Processing helix chain 'I' and resid 97 through 106 removed outlier: 3.633A pdb=" N PHE I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 131 removed outlier: 3.541A pdb=" N THR I 114 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 149 removed outlier: 3.843A pdb=" N TYR I 148 " --> pdb=" O PRO I 144 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS I 149 " --> pdb=" O GLU I 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 144 through 149' Processing helix chain 'I' and resid 204 through 218 Processing helix chain 'I' and resid 226 through 230 Processing helix chain 'I' and resid 248 through 264 removed outlier: 3.702A pdb=" N ALA I 253 " --> pdb=" O GLU I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 351 Processing helix chain 'I' and resid 366 through 377 Processing helix chain 'I' and resid 451 through 464 removed outlier: 3.577A pdb=" N VAL I 455 " --> pdb=" O GLU I 451 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU I 456 " --> pdb=" O ILE I 452 " (cutoff:3.500A) Processing helix chain 'I' and resid 477 through 491 removed outlier: 3.637A pdb=" N ARG I 481 " --> pdb=" O PRO I 477 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA I 483 " --> pdb=" O THR I 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 22 through 30 removed outlier: 3.996A pdb=" N ALA E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 60 Processing helix chain 'E' and resid 77 through 83 Processing helix chain 'E' and resid 97 through 106 Processing helix chain 'E' and resid 110 through 131 removed outlier: 3.532A pdb=" N TYR E 115 " --> pdb=" O HIS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 226 through 230 Processing helix chain 'E' and resid 248 through 264 removed outlier: 3.928A pdb=" N ALA E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP E 254 " --> pdb=" O GLY E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 291 No H-bonds generated for 'chain 'E' and resid 289 through 291' Processing helix chain 'E' and resid 331 through 351 removed outlier: 3.662A pdb=" N GLN E 349 " --> pdb=" O SER E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 377 removed outlier: 3.529A pdb=" N ASN E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 464 Processing helix chain 'E' and resid 477 through 492 removed outlier: 3.703A pdb=" N ARG E 481 " --> pdb=" O PRO E 477 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 507 removed outlier: 4.057A pdb=" N TYR E 506 " --> pdb=" O ALA E 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 29 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 71 through 89 removed outlier: 3.561A pdb=" N HIS D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 139 removed outlier: 3.528A pdb=" N GLY D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 158 removed outlier: 3.752A pdb=" N TYR D 154 " --> pdb=" O SER D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 257 through 277 removed outlier: 3.951A pdb=" N GLN D 262 " --> pdb=" O ASN D 258 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN D 267 " --> pdb=" O ARG D 263 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU D 274 " --> pdb=" O ASN D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 300 through 304 removed outlier: 3.820A pdb=" N ASP D 303 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.995A pdb=" N SER D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 385 removed outlier: 3.586A pdb=" N LEU D 384 " --> pdb=" O PHE D 380 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 28 Processing helix chain 'B' and resid 48 through 56 Processing helix chain 'B' and resid 72 through 89 Processing helix chain 'B' and resid 123 through 139 Processing helix chain 'B' and resid 147 through 159 removed outlier: 4.009A pdb=" N ASN B 151 " --> pdb=" O HIS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.548A pdb=" N ARG B 263 " --> pdb=" O TYR B 259 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.526A pdb=" N LYS B 304 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.957A pdb=" N SER B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 371 through 384 removed outlier: 3.724A pdb=" N LYS B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 22 through 30 Processing helix chain 'C' and resid 46 through 61 removed outlier: 3.518A pdb=" N GLN C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 83 Processing helix chain 'C' and resid 97 through 105 removed outlier: 3.533A pdb=" N ILE C 101 " --> pdb=" O THR C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 131 Processing helix chain 'C' and resid 204 through 218 removed outlier: 4.063A pdb=" N GLU C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N HIS C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 248 through 264 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 366 through 377 Processing helix chain 'C' and resid 451 through 464 Processing helix chain 'C' and resid 477 through 491 removed outlier: 3.697A pdb=" N ARG C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 28 removed outlier: 3.772A pdb=" N ASP F 15 " --> pdb=" O THR F 11 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ASP F 16 " --> pdb=" O PRO F 12 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR F 18 " --> pdb=" O ASP F 14 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU F 28 " --> pdb=" O LYS F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 56 Processing helix chain 'F' and resid 71 through 89 removed outlier: 3.640A pdb=" N HIS F 87 " --> pdb=" O LYS F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 138 Processing helix chain 'F' and resid 150 through 162 removed outlier: 3.534A pdb=" N ILE F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS F 162 " --> pdb=" O PHE F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 245 No H-bonds generated for 'chain 'F' and resid 243 through 245' Processing helix chain 'F' and resid 257 through 277 removed outlier: 4.275A pdb=" N MET F 277 " --> pdb=" O PHE F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 removed outlier: 3.945A pdb=" N LYS F 304 " --> pdb=" O GLU F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 365 removed outlier: 3.605A pdb=" N HIS F 358 " --> pdb=" O LYS F 354 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS F 363 " --> pdb=" O SER F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 384 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 30 Processing helix chain 'G' and resid 46 through 61 Processing helix chain 'G' and resid 77 through 83 Processing helix chain 'G' and resid 97 through 105 Processing helix chain 'G' and resid 112 through 131 removed outlier: 3.860A pdb=" N VAL G 118 " --> pdb=" O THR G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 216 Processing helix chain 'G' and resid 226 through 230 Processing helix chain 'G' and resid 248 through 264 Processing helix chain 'G' and resid 331 through 351 Processing helix chain 'G' and resid 366 through 377 Processing helix chain 'G' and resid 451 through 465 removed outlier: 3.631A pdb=" N VAL G 455 " --> pdb=" O GLU G 451 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU G 456 " --> pdb=" O ILE G 452 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU G 465 " --> pdb=" O ALA G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 477 through 493 removed outlier: 3.748A pdb=" N ARG G 481 " --> pdb=" O PRO G 477 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 483 " --> pdb=" O THR G 479 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER G 493 " --> pdb=" O ILE G 489 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 32 through 33 removed outlier: 3.519A pdb=" N TRP H 33 " --> pdb=" O ILE H 5 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS H 4 " --> pdb=" O CYS H 58 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE H 60 " --> pdb=" O LYS H 4 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE H 6 " --> pdb=" O PHE H 60 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE H 62 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER H 8 " --> pdb=" O ILE H 62 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N SER H 64 " --> pdb=" O SER H 8 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ILE H 118 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 295 through 299 removed outlier: 5.698A pdb=" N VAL I 278 " --> pdb=" O LEU I 305 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU I 305 " --> pdb=" O VAL I 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 295 through 299 removed outlier: 6.128A pdb=" N CYS I 279 " --> pdb=" O PHE I 358 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N HIS I 360 " --> pdb=" O CYS I 279 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU I 281 " --> pdb=" O HIS I 360 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS I 417 " --> pdb=" O VAL I 413 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE I 412 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU I 3 " --> pdb=" O ILE I 412 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS I 2 " --> pdb=" O LYS H 409 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 326 through 328 removed outlier: 7.153A pdb=" N LEU H 402 " --> pdb=" O ILE H 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 184 through 187 Processing sheet with id=AA6, first strand: chain 'H' and resid 283 through 286 Processing sheet with id=AA7, first strand: chain 'H' and resid 283 through 286 Processing sheet with id=AA8, first strand: chain 'I' and resid 19 through 20 Processing sheet with id=AA9, first strand: chain 'I' and resid 91 through 95 removed outlier: 6.308A pdb=" N GLY I 42 " --> pdb=" O PHE I 140 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE I 142 " --> pdb=" O GLY I 42 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL I 44 " --> pdb=" O ILE I 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 425 through 426 removed outlier: 3.844A pdb=" N SER I 431 " --> pdb=" O VAL I 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 311 through 320 removed outlier: 5.846A pdb=" N GLY E 318 " --> pdb=" O CYS E 298 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N CYS E 298 " --> pdb=" O GLY E 318 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TRP E 320 " --> pdb=" O ASN E 296 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN E 296 " --> pdb=" O TRP E 320 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA E 301 " --> pdb=" O GLY E 282 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR E 280 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N CYS E 279 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N HIS E 360 " --> pdb=" O CYS E 279 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU E 281 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR E 387 " --> pdb=" O ILE E 445 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE E 445 " --> pdb=" O THR E 387 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR E 389 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE E 443 " --> pdb=" O THR E 389 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYS E 417 " --> pdb=" O VAL E 413 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE E 412 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLU E 3 " --> pdb=" O ILE E 412 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LYS E 2 " --> pdb=" O PHE D 411 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU D 169 " --> pdb=" O GLY D 412 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AB4, first strand: chain 'E' and resid 91 through 95 removed outlier: 3.627A pdb=" N GLY E 45 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLY E 42 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE E 142 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL E 44 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TRP E 139 " --> pdb=" O GLN E 222 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU E 224 " --> pdb=" O TRP E 139 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL E 141 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 425 through 426 removed outlier: 3.592A pdb=" N SER E 431 " --> pdb=" O VAL E 426 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 32 through 33 removed outlier: 6.173A pdb=" N ILE D 5 " --> pdb=" O TRP D 33 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LYS D 4 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU D 61 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE D 6 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL D 63 " --> pdb=" O PHE D 6 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N SER D 8 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE D 62 " --> pdb=" O ILE D 95 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 327 through 328 removed outlier: 3.529A pdb=" N LYS D 328 " --> pdb=" O VAL D 334 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU D 402 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 184 through 187 Processing sheet with id=AB9, first strand: chain 'D' and resid 283 through 286 Processing sheet with id=AC1, first strand: chain 'D' and resid 283 through 286 Processing sheet with id=AC2, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.418A pdb=" N ILE B 5 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS B 4 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LEU B 61 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE B 6 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL B 63 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N SER B 8 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 62 " --> pdb=" O ILE B 95 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 409 through 412 Processing sheet with id=AC4, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.508A pdb=" N PHE B 176 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU B 402 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 403 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 285 through 286 Processing sheet with id=AC6, first strand: chain 'C' and resid 5 through 6 removed outlier: 6.579A pdb=" N LYS C 417 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N CYS C 279 " --> pdb=" O PHE C 358 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N HIS C 360 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU C 281 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL C 278 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU C 305 " --> pdb=" O VAL C 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 5 through 6 removed outlier: 6.579A pdb=" N LYS C 417 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N CYS C 279 " --> pdb=" O PHE C 358 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N HIS C 360 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU C 281 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP C 320 " --> pdb=" O CYS C 298 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.508A pdb=" N LYS C 270 " --> pdb=" O LEU C 13 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 91 through 95 removed outlier: 6.293A pdb=" N GLY C 42 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE C 142 " --> pdb=" O GLY C 42 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C 44 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP C 139 " --> pdb=" O GLN C 222 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU C 224 " --> pdb=" O TRP C 139 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL C 141 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 235 through 236 removed outlier: 3.511A pdb=" N ASN C 236 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 425 through 426 removed outlier: 3.736A pdb=" N SER C 431 " --> pdb=" O VAL C 426 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 32 through 34 removed outlier: 3.583A pdb=" N ILE F 62 " --> pdb=" O ILE F 95 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 409 through 412 Processing sheet with id=AD5, first strand: chain 'F' and resid 293 through 294 removed outlier: 6.823A pdb=" N LEU F 402 " --> pdb=" O ILE F 179 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 217 through 218 removed outlier: 3.602A pdb=" N ALA F 218 " --> pdb=" O ARG F 186 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 5 through 6 removed outlier: 5.205A pdb=" N ILE G 443 " --> pdb=" O THR G 389 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR G 389 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE G 445 " --> pdb=" O THR G 387 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR G 387 " --> pdb=" O ILE G 445 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N CYS G 279 " --> pdb=" O PHE G 358 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N HIS G 360 " --> pdb=" O CYS G 279 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU G 281 " --> pdb=" O HIS G 360 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL G 278 " --> pdb=" O LEU G 305 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU G 305 " --> pdb=" O VAL G 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 5 through 6 removed outlier: 5.205A pdb=" N ILE G 443 " --> pdb=" O THR G 389 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR G 389 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE G 445 " --> pdb=" O THR G 387 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR G 387 " --> pdb=" O ILE G 445 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N CYS G 279 " --> pdb=" O PHE G 358 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N HIS G 360 " --> pdb=" O CYS G 279 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N LEU G 281 " --> pdb=" O HIS G 360 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL G 278 " --> pdb=" O LEU G 305 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU G 305 " --> pdb=" O VAL G 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 19 through 20 Processing sheet with id=AE1, first strand: chain 'G' and resid 91 through 95 removed outlier: 3.520A pdb=" N VAL G 92 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY G 42 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE G 142 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL G 44 " --> pdb=" O ILE G 142 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 235 through 236 Processing sheet with id=AE3, first strand: chain 'G' and resid 425 through 426 removed outlier: 3.845A pdb=" N SER G 431 " --> pdb=" O VAL G 426 " (cutoff:3.500A) 1133 hydrogen bonds defined for protein. 3207 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 101 stacking parallelities Total time for adding SS restraints: 5.99 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5024 1.33 - 1.45: 8660 1.45 - 1.57: 16611 1.57 - 1.69: 289 1.69 - 1.81: 103 Bond restraints: 30687 Sorted by residual: bond pdb=" N GLU E 476 " pdb=" CA GLU E 476 " ideal model delta sigma weight residual 1.456 1.500 -0.044 9.80e-03 1.04e+04 2.04e+01 bond pdb=" C ALA F 10 " pdb=" O ALA F 10 " ideal model delta sigma weight residual 1.232 1.289 -0.057 1.37e-02 5.33e+03 1.74e+01 bond pdb=" N SER F 8 " pdb=" CA SER F 8 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.87e+00 bond pdb=" N HIS F 9 " pdb=" CA HIS F 9 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.69e+00 bond pdb=" C GLU E 476 " pdb=" N PRO E 477 " ideal model delta sigma weight residual 1.332 1.364 -0.032 1.30e-02 5.92e+03 6.15e+00 ... (remaining 30682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 42119 3.19 - 6.38: 197 6.38 - 9.57: 23 9.57 - 12.76: 5 12.76 - 15.95: 1 Bond angle restraints: 42345 Sorted by residual: angle pdb=" O3' DA V 4 " pdb=" P DT V 5 " pdb=" O5' DT V 5 " ideal model delta sigma weight residual 104.00 119.95 -15.95 1.50e+00 4.44e-01 1.13e+02 angle pdb=" N ILE I 36 " pdb=" CA ILE I 36 " pdb=" C ILE I 36 " ideal model delta sigma weight residual 108.97 96.32 12.65 1.55e+00 4.16e-01 6.66e+01 angle pdb=" N ASP F 14 " pdb=" CA ASP F 14 " pdb=" C ASP F 14 " ideal model delta sigma weight residual 111.30 100.74 10.56 1.43e+00 4.89e-01 5.46e+01 angle pdb=" N LEU D 214 " pdb=" CA LEU D 214 " pdb=" C LEU D 214 " ideal model delta sigma weight residual 111.54 101.54 10.00 1.36e+00 5.41e-01 5.41e+01 angle pdb=" C TYR F 190 " pdb=" CA TYR F 190 " pdb=" CB TYR F 190 " ideal model delta sigma weight residual 111.73 120.17 -8.44 1.42e+00 4.96e-01 3.53e+01 ... (remaining 42340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.92: 16554 28.92 - 57.83: 1346 57.83 - 86.75: 161 86.75 - 115.66: 3 115.66 - 144.58: 4 Dihedral angle restraints: 18068 sinusoidal: 7912 harmonic: 10156 Sorted by residual: dihedral pdb=" CD ARG H 189 " pdb=" NE ARG H 189 " pdb=" CZ ARG H 189 " pdb=" NH1 ARG H 189 " ideal model delta sinusoidal sigma weight residual 0.00 -80.86 80.86 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CA MET F 277 " pdb=" C MET F 277 " pdb=" N LYS F 278 " pdb=" CA LYS F 278 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA GLY E 318 " pdb=" C GLY E 318 " pdb=" N PRO E 319 " pdb=" CA PRO E 319 " ideal model delta harmonic sigma weight residual -180.00 -153.33 -26.67 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 18065 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 4857 0.161 - 0.322: 3 0.322 - 0.484: 1 0.484 - 0.645: 3 0.645 - 0.806: 1 Chirality restraints: 4865 Sorted by residual: chirality pdb=" P DT V 5 " pdb=" OP1 DT V 5 " pdb=" OP2 DT V 5 " pdb=" O5' DT V 5 " both_signs ideal model delta sigma weight residual True 2.35 -3.15 -0.81 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" P DT T 5 " pdb=" OP1 DT T 5 " pdb=" OP2 DT T 5 " pdb=" O5' DT T 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.62 2.00e-01 2.50e+01 9.47e+00 chirality pdb=" P DT N 5 " pdb=" OP1 DT N 5 " pdb=" OP2 DT N 5 " pdb=" O5' DT N 5 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.55e+00 ... (remaining 4862 not shown) Planarity restraints: 4793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 189 " 1.079 9.50e-02 1.11e+02 4.83e-01 1.41e+02 pdb=" NE ARG H 189 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG H 189 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG H 189 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG H 189 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS G 62 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO G 63 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO G 63 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 63 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 181 " -0.047 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO B 182 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 182 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 182 " -0.039 5.00e-02 4.00e+02 ... (remaining 4790 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 495 2.65 - 3.22: 25548 3.22 - 3.78: 43886 3.78 - 4.34: 62222 4.34 - 4.90: 101791 Nonbonded interactions: 233942 Sorted by model distance: nonbonded pdb=" OP1 U X 1 " pdb="MG MG G 601 " model vdw 2.092 2.170 nonbonded pdb=" OD1 ASP E 414 " pdb=" N GLU E 415 " model vdw 2.151 3.120 nonbonded pdb=" OP1 A M 3 " pdb="MG MG E 601 " model vdw 2.166 2.170 nonbonded pdb=" OP1 U U 1 " pdb="MG MG C 601 " model vdw 2.190 2.170 nonbonded pdb=" OG1 THR H 344 " pdb=" O ASN H 349 " model vdw 2.198 3.040 ... (remaining 233937 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 7 or (resid 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 11 or (resid 12 through 16 and (name N or name CA \ or name C or name O or name CB )) or resid 17 through 23 or (resid 24 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name CE )) \ or resid 25 through 37 or (resid 38 and (name N or name CA or name C or name O \ or name CB )) or resid 46 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB or name CG or name CD )) or resid 60 through 65 or (resi \ d 66 through 67 and (name N or name CA or name C or name O or name CB )) or resi \ d 68 through 69 or (resid 70 and (name N or name CA or name C or name O or name \ CB )) or resid 71 through 76 or (resid 77 and (name N or name CA or name C or na \ me O or name CB )) or resid 78 through 91 or (resid 92 and (name N or name CA or \ name C or name O or name CB )) or resid 93 through 98 or (resid 99 and (name N \ or name CA or name C or name O or name CB or name CG1 or name CG2)) or resid 100 \ through 103 or (resid 104 and (name N or name CA or name C or name O or name CB \ )) or resid 105 through 106 or (resid 107 and (name N or name CA or name C or n \ ame O or name CB )) or resid 108 through 113 or (resid 114 and (name N or name C \ A or name C or name O or name CB )) or resid 115 or (resid 116 through 117 and ( \ name N or name CA or name C or name O or name CB )) or resid 118 through 120 or \ (resid 121 through 122 and (name N or name CA or name C or name O or name CB )) \ or resid 123 through 129 or (resid 130 and (name N or name CA or name C or name \ O or name CB )) or resid 131 through 136 or (resid 137 and (name N or name CA or \ name C or name O or name CB )) or resid 138 or (resid 139 and (name N or name C \ A or name C or name O or name CB or name CG )) or resid 140 through 143 or (resi \ d 149 through 152 and (name N or name CA or name C or name O or name CB )) or re \ sid 153 or (resid 154 through 155 and (name N or name CA or name C or name O or \ name CB )) or resid 156 through 157 or (resid 158 and (name N or name CA or name \ C or name O or name CB )) or resid 159 through 162 or (resid 163 through 164 an \ d (name N or name CA or name C or name O or name CB )) or resid 165 through 167 \ or (resid 168 through 169 and (name N or name CA or name C or name O or name CB \ )) or resid 170 through 183 or (resid 184 and (name N or name CA or name C or na \ me O or name CB )) or resid 185 through 188 or (resid 189 and (name N or name CA \ or name C or name O or name CB )) or (resid 190 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE \ 2 or name CZ )) or resid 191 through 198 or (resid 199 through 200 and (name N o \ r name CA or name C or name O or name CB )) or resid 201 through 226 or (resid 2 \ 27 through 234 and (name N or name CA or name C or name O or name CB )) or resid \ 235 through 256 or (resid 257 and (name N or name CA or name C or name O or nam \ e CB )) or resid 258 or (resid 259 and (name N or name CA or name C or name O or \ name CB )) or (resid 260 and (name N or name CA or name C or name O or name CB \ or name CG or name CD )) or resid 261 through 277 or (resid 278 through 279 and \ (name N or name CA or name C or name O or name CB )) or resid 280 through 283 or \ (resid 284 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 5 through 295 or (resid 296 through 297 and (name N or name CA or name C or name \ O or name CB )) or resid 298 or (resid 299 and (name N or name CA or name C or \ name O or name CB )) or resid 300 through 305 or (resid 306 through 307 and (nam \ e N or name CA or name C or name O or name CB )) or resid 308 through 327 or (re \ sid 328 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE )) or resid 329 through 347 or (resid 348 through 349 and (name N \ or name CA or name C or name O or name CB )) or resid 350 through 353 or (resid \ 354 and (name N or name CA or name C or name O or name CB )) or resid 355 throu \ gh 358 or (resid 359 and (name N or name CA or name C or name O or name CB )) or \ resid 360 through 362 or (resid 363 and (name N or name CA or name C or name O \ or name CB or name CG or name CD )) or resid 364 through 396 or (resid 397 throu \ gh 398 and (name N or name CA or name C or name O or name CB )) or resid 399 thr \ ough 420)) selection = (chain 'D' and (resid 3 through 11 or (resid 12 through 16 and (name N or name C \ A or name C or name O or name CB )) or resid 17 through 23 or (resid 24 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE ) \ ) or resid 25 through 47 or (resid 48 and (name N or name CA or name C or name O \ or name CB )) or resid 49 through 50 or (resid 51 through 52 and (name N or nam \ e CA or name C or name O or name CB )) or resid 53 or (resid 54 through 55 and ( \ name N or name CA or name C or name O or name CB )) or resid 56 through 58 or (r \ esid 59 and (name N or name CA or name C or name O or name CB or name CG or name \ CD )) or resid 60 through 65 or (resid 66 through 67 and (name N or name CA or \ name C or name O or name CB )) or resid 68 through 70 or (resid 71 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD or name NE )) or \ resid 72 through 75 or (resid 76 through 77 and (name N or name CA or name C or \ name O or name CB )) or resid 78 through 82 or (resid 83 and (name N or name CA \ or name C or name O or name CB or name CG or name CD )) or resid 84 through 91 o \ r (resid 92 and (name N or name CA or name C or name O or name CB )) or resid 93 \ through 99 or (resid 100 through 102 and (name N or name CA or name C or name O \ or name CB )) or resid 103 or (resid 104 and (name N or name CA or name C or na \ me O or name CB )) or resid 105 through 106 or (resid 107 and (name N or name CA \ or name C or name O or name CB )) or resid 108 through 109 or (resid 110 and (n \ ame N or name CA or name C or name O or name CB or name CG1 or name CG2)) or (re \ sid 111 and (name N or name CA or name C or name O or name CB )) or resid 112 th \ rough 113 or (resid 114 and (name N or name CA or name C or name O or name CB )) \ or resid 115 or (resid 116 through 117 and (name N or name CA or name C or name \ O or name CB )) or resid 118 through 120 or (resid 121 through 122 and (name N \ or name CA or name C or name O or name CB )) or resid 123 through 129 or (resid \ 130 and (name N or name CA or name C or name O or name CB )) or resid 131 throug \ h 136 or (resid 137 and (name N or name CA or name C or name O or name CB )) or \ (resid 138 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD )) or (resid 139 and (name N or name CA or name C or name O or name CB or \ name CG )) or resid 140 through 143 or (resid 149 through 152 and (name N or na \ me CA or name C or name O or name CB )) or resid 153 or (resid 154 through 155 a \ nd (name N or name CA or name C or name O or name CB )) or resid 156 through 157 \ or (resid 158 and (name N or name CA or name C or name O or name CB )) or resid \ 159 through 161 or (resid 162 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name CE )) or (resid 163 through 164 and (name N o \ r name CA or name C or name O or name CB )) or resid 165 through 167 or (resid 1 \ 68 through 169 and (name N or name CA or name C or name O or name CB )) or resid \ 170 through 188 or (resid 189 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 190 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 19 \ 1 through 192 or (resid 193 and (name N or name CA or name C or name O or name C \ B )) or resid 194 through 198 or (resid 199 through 200 and (name N or name CA o \ r name C or name O or name CB )) or resid 201 through 210 or (resid 211 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE ) \ ) or resid 212 through 226 or (resid 227 through 234 and (name N or name CA or n \ ame C or name O or name CB )) or (resid 235 through 237 and (name N or name CA o \ r name C or name O or name CB )) or resid 238 through 242 or (resid 243 through \ 244 and (name N or name CA or name C or name O or name CB )) or resid 245 throug \ h 256 or (resid 257 and (name N or name CA or name C or name O or name CB )) or \ resid 258 or (resid 259 and (name N or name CA or name C or name O or name CB )) \ or (resid 260 and (name N or name CA or name C or name O or name CB or name CG \ or name CD )) or resid 261 through 283 or (resid 284 and (name N or name CA or n \ ame C or name O or name CB )) or resid 285 through 312 or (resid 313 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE )) o \ r resid 314 through 345 or (resid 346 and (name N or name CA or name C or name O \ or name CB )) or (resid 347 through 349 and (name N or name CA or name C or nam \ e O or name CB )) or resid 350 through 353 or (resid 354 and (name N or name CA \ or name C or name O or name CB )) or resid 355 through 370 or (resid 371 and (na \ me N or name CA or name C or name O or name CB )) or resid 372 through 390 or (r \ esid 391 and (name N or name CA or name C or name O or name CB or name CG1 or na \ me CG2)) or resid 392 through 412 or (resid 413 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or resid 414 through 420)) selection = (chain 'F' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 7 or (resid 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 through 18 or (resid 19 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name NE )) or resid 2 \ 0 through 23 or (resid 24 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE )) or resid 25 through 30 or (resid 31 and (nam \ e N or name CA or name C or name O or name CB )) or resid 32 through 34 or (resi \ d 35 and (name N or name CA or name C or name O or name CB )) or resid 36 throug \ h 37 or (resid 38 and (name N or name CA or name C or name O or name CB )) or re \ sid 46 through 47 or (resid 48 and (name N or name CA or name C or name O or nam \ e CB )) or resid 49 or (resid 50 through 52 and (name N or name CA or name C or \ name O or name CB )) or resid 53 or (resid 54 through 55 and (name N or name CA \ or name C or name O or name CB )) or resid 56 through 58 or (resid 59 and (name \ N or name CA or name C or name O or name CB or name CG or name CD )) or resid 60 \ through 65 or (resid 66 through 67 and (name N or name CA or name C or name O o \ r name CB )) or resid 68 through 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or (resid 71 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE )) or resid 72 through 75 or (resi \ d 76 through 77 and (name N or name CA or name C or name O or name CB )) or resi \ d 78 through 82 or (resid 83 and (name N or name CA or name C or name O or name \ CB or name CG or name CD )) or resid 84 through 98 or (resid 99 and (name N or n \ ame CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 100 th \ rough 102 and (name N or name CA or name C or name O or name CB )) or resid 103 \ through 106 or (resid 107 and (name N or name CA or name C or name O or name CB \ )) or resid 108 through 110 or (resid 111 and (name N or name CA or name C or na \ me O or name CB )) or (resid 112 through 113 and (name N or name CA or name C or \ name O or name CB or name CG1 or name CG2)) or (resid 114 and (name N or name C \ A or name C or name O or name CB )) or resid 115 through 120 or (resid 121 throu \ gh 122 and (name N or name CA or name C or name O or name CB )) or resid 123 thr \ ough 125 or (resid 126 and (name N or name CA or name C or name O or name CB )) \ or resid 127 through 129 or (resid 130 and (name N or name CA or name C or name \ O or name CB )) or resid 131 through 137 or (resid 138 and (name N or name CA or \ name C or name O or name CB or name CG or name CD )) or resid 139 through 143 o \ r (resid 149 through 152 and (name N or name CA or name C or name O or name CB ) \ ) or resid 153 or (resid 154 through 155 and (name N or name CA or name C or nam \ e O or name CB )) or resid 156 through 157 or (resid 158 and (name N or name CA \ or name C or name O or name CB )) or resid 159 or (resid 160 through 161 and (na \ me N or name CA or name C or name O or name CB )) or resid 162 through 165 or (r \ esid 166 and (name N or name CA or name C or name O or name CB )) or resid 167 o \ r (resid 168 through 169 and (name N or name CA or name C or name O or name CB ) \ ) or resid 170 through 183 or (resid 184 and (name N or name CA or name C or nam \ e O or name CB )) or resid 185 through 225 or (resid 226 through 234 and (name N \ or name CA or name C or name O or name CB )) or resid 235 through 242 or (resid \ 243 through 244 and (name N or name CA or name C or name O or name CB )) or res \ id 245 through 295 or (resid 296 through 297 and (name N or name CA or name C or \ name O or name CB )) or resid 298 or (resid 299 and (name N or name CA or name \ C or name O or name CB )) or resid 300 through 305 or (resid 306 through 307 and \ (name N or name CA or name C or name O or name CB )) or resid 308 through 312 o \ r (resid 313 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name CE )) or resid 314 through 347 or (resid 348 through 349 and (n \ ame N or name CA or name C or name O or name CB )) or resid 350 through 353 or ( \ resid 354 and (name N or name CA or name C or name O or name CB )) or resid 355 \ through 358 or (resid 359 and (name N or name CA or name C or name O or name CB \ )) or resid 360 through 370 or (resid 371 and (name N or name CA or name C or na \ me O or name CB )) or resid 372 through 390 or (resid 391 and (name N or name CA \ or name C or name O or name CB or name CG1 or name CG2)) or resid 392 through 3 \ 96 or (resid 397 through 398 and (name N or name CA or name C or name O or name \ CB )) or resid 399 through 412 or (resid 413 and (name N or name CA or name C or \ name O or name CB or name CG or name CD )) or resid 414 through 420)) selection = (chain 'H' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 7 or (resid 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 11 or (resid 12 through 16 and (name N or name CA \ or name C or name O or name CB )) or resid 17 through 18 or (resid 19 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name NE )) \ or resid 20 through 30 or (resid 31 and (name N or name CA or name C or name O \ or name CB )) or resid 32 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 46 through 47 or (resid 48 and (name N or na \ me CA or name C or name O or name CB )) or resid 49 or (resid 50 through 52 and \ (name N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 th \ rough 55 and (name N or name CA or name C or name O or name CB )) or resid 56 th \ rough 69 or (resid 70 and (name N or name CA or name C or name O or name CB )) o \ r (resid 71 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name NE )) or resid 72 through 75 or (resid 76 through 77 and (name N \ or name CA or name C or name O or name CB )) or resid 78 through 82 or (resid 8 \ 3 and (name N or name CA or name C or name O or name CB or name CG or name CD )) \ or resid 84 through 98 or (resid 99 and (name N or name CA or name C or name O \ or name CB or name CG1 or name CG2)) or (resid 100 through 102 and (name N or na \ me CA or name C or name O or name CB )) or resid 103 through 109 or (resid 110 a \ nd (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) o \ r resid 111 or (resid 112 through 113 and (name N or name CA or name C or name O \ or name CB or name CG1 or name CG2)) or resid 114 through 137 or (resid 138 and \ (name N or name CA or name C or name O or name CB or name CG or name CD )) or ( \ resid 139 and (name N or name CA or name C or name O or name CB or name CG )) or \ resid 140 through 143 or (resid 149 through 152 and (name N or name CA or name \ C or name O or name CB )) or resid 153 through 159 or (resid 160 through 161 and \ (name N or name CA or name C or name O or name CB )) or (resid 162 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name CE )) or \ resid 163 through 188 or (resid 189 and (name N or name CA or name C or name O \ or name CB )) or (resid 190 and (name N or name CA or name C or name O or name C \ B or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or re \ sid 191 through 192 or (resid 193 and (name N or name CA or name C or name O or \ name CB )) or resid 194 through 198 or (resid 199 through 200 and (name N or nam \ e CA or name C or name O or name CB )) or resid 201 through 210 or (resid 211 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e CE )) or resid 212 through 225 or (resid 226 through 234 and (name N or name C \ A or name C or name O or name CB )) or (resid 235 through 237 and (name N or nam \ e CA or name C or name O or name CB )) or resid 238 through 242 or (resid 243 th \ rough 244 and (name N or name CA or name C or name O or name CB )) or resid 245 \ through 256 or (resid 257 and (name N or name CA or name C or name O or name CB \ )) or resid 258 or (resid 259 and (name N or name CA or name C or name O or name \ CB )) or (resid 260 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD )) or resid 261 through 283 or (resid 284 and (name N or name C \ A or name C or name O or name CB )) or resid 285 through 295 or (resid 296 throu \ gh 297 and (name N or name CA or name C or name O or name CB )) or resid 298 thr \ ough 312 or (resid 313 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name CE )) or resid 314 through 327 or (resid 328 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD or name CE ) \ ) or resid 329 through 358 or (resid 359 and (name N or name CA or name C or nam \ e O or name CB )) or resid 360 through 362 or (resid 363 and (name N or name CA \ or name C or name O or name CB or name CG or name CD )) or resid 364 through 370 \ or (resid 371 and (name N or name CA or name C or name O or name CB )) or resid \ 372 through 390 or (resid 391 and (name N or name CA or name C or name O or nam \ e CB or name CG1 or name CG2)) or resid 392 through 396 or (resid 397 through 39 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 399 through \ 412 or (resid 413 and (name N or name CA or name C or name O or name CB or name \ CG or name CD )) or resid 414 through 420)) } ncs_group { reference = (chain 'C' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB or name CG )) or resid 4 through 7 or (resid 8 and (name N o \ r name CA or name C or name O or name CB )) or resid 9 through 34 or (resid 35 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD )) or \ resid 36 through 40 or (resid 41 and (name N or name CA or name C or name O or \ name CB )) or resid 42 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 50 or (resid 51 and (name N or name \ CA or name C or name O or name CB )) or (resid 52 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2)) or resid 53 through 57 or (res \ id 58 and (name N or name CA or name C or name O or name CB )) or (resid 59 and \ (name N or name CA or name C or name O or name CB or name CG or name CD )) or re \ sid 60 through 61 or (resid 62 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD or name CE )) or resid 63 through 67 or (resid 68 and \ (name N or name CA or name C or name O or name CB or name CG )) or resid 69 thr \ ough 71 or (resid 72 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name NE or name CZ )) or resid 73 through 84 or (resid 85 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e CE )) or resid 86 through 100 or (resid 101 through 102 and (name N or name CA \ or name C or name O or name CB )) or resid 103 or (resid 104 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name C \ E1 or name CE2 or name CZ )) or resid 105 through 106 or (resid 109 through 112 \ and (name N or name CA or name C or name O or name CB )) or resid 113 through 12 \ 2 or (resid 123 and (name N or name CA or name C or name O or name CB )) or resi \ d 124 through 133 or (resid 134 and (name N or name CA or name C or name O or na \ me CB )) or resid 135 through 147 or (resid 148 through 149 and (name N or name \ CA or name C or name O or name CB )) or resid 205 through 207 or (resid 208 and \ (name N or name CA or name C or name O or name CB )) or resid 209 through 215 or \ (resid 216 and (name N or name CA or name C or name O or name CB )) or resid 21 \ 7 through 242 or resid 244 through 247 or (resid 248 and (name N or name CA or n \ ame C or name O or name CB or name CG1 or name CG2)) or resid 249 through 262 or \ (resid 263 and (name N or name CA or name C or name O or name CB or name CG or \ name CD or name CE )) or resid 264 through 266 or resid 268 through 302 or (resi \ d 303 and (name N or name CA or name C or name O or name CB or name CG or name S \ D )) or resid 304 through 330 or (resid 331 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name CE )) or resid 332 through 347 o \ r (resid 348 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 49 through 351 or (resid 352 and (name N or name CA or name C or name O or name \ CB )) or resid 353 through 355 or (resid 356 and (name N or name CA or name C or \ name O or name CB )) or resid 357 through 367 or (resid 368 and (name N or name \ CA or name C or name O or name CB or name CG )) or resid 369 through 410 or (re \ sid 411 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 412 through 414 \ or (resid 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 430 or (resid 431 and (name N or name CA or name C or name O or name \ CB )) or resid 432 through 473 or (resid 474 and (name N or name CA or name C o \ r name O or name CB )) or resid 475 through 484 or (resid 485 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD or name CE )) or resid \ 486 through 493 or (resid 494 through 495 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 496 and (name N or name CA or name C or name O or \ name CB or name CG1 or name CG2)) or (resid 497 through 498 and (name N or name \ CA or name C or name O or name CB )) or resid 499 through 506 or (resid 507 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) or r \ esid 601)) selection = (chain 'E' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD )) or resid 3 through 69 or (resid 70 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2)) or resid 7 \ 1 through 95 or (resid 96 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2)) or resid 97 through 106 or resid 109 through 112 or (r \ esid 113 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name NE )) or resid 114 through 145 or (resid 146 and (name N or name CA \ or name C or name O or name CB )) or resid 147 through 234 or (resid 235 throug \ h 238 and (name N or name CA or name C or name O or name CB )) or resid 239 thro \ ugh 241 or (resid 242 and (name N or name CA or name C or name O or name CB )) o \ r resid 244 through 266 or resid 268 through 290 or resid 293 through 305 or (re \ sid 306 and (name N or name CA or name C or name O or name CB )) or resid 307 th \ rough 324 or (resid 325 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name CE )) or resid 326 through 332 or (resid 333 and (na \ me N or name CA or name C or name O or name CB )) or resid 334 through 350 or (r \ esid 351 through 352 and (name N or name CA or name C or name O or name CB )) or \ resid 353 through 354 or (resid 355 and (name N or name CA or name C or name O \ or name CB or name CG or name CD )) or (resid 356 and (name N or name CA or name \ C or name O or name CB )) or resid 357 through 367 or (resid 368 and (name N or \ name CA or name C or name O or name CB or name CG )) or resid 369 through 414 o \ r (resid 415 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 16 through 427 or (resid 428 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name CE )) or resid 429 through 601)) selection = (chain 'G' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD )) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 4 through 7 or (resid 8 and (name N \ or name CA or name C or name O or name CB )) or resid 9 through 40 or (resid 41 \ and (name N or name CA or name C or name O or name CB )) or resid 42 through 47 \ or (resid 48 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 9 through 50 or (resid 51 and (name N or name CA or name C or name O or name CB \ )) or (resid 52 and (name N or name CA or name C or name O or name CB or name CG \ 1 or name CG2)) or resid 53 through 57 or (resid 58 and (name N or name CA or na \ me C or name O or name CB )) or (resid 59 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD )) or resid 60 through 61 or (resid 62 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ CE )) or resid 63 through 67 or (resid 68 and (name N or name CA or name C or n \ ame O or name CB or name CG )) or resid 69 through 71 or (resid 72 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD or name NE or nam \ e CZ )) or resid 73 through 84 or (resid 85 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name CE )) or resid 86 through 100 or \ (resid 101 through 102 and (name N or name CA or name C or name O or name CB )) \ or resid 103 or (resid 104 and (name N or name CA or name C or name O or name C \ B or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or re \ sid 105 through 106 or (resid 109 through 112 and (name N or name CA or name C o \ r name O or name CB )) or (resid 113 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name NE )) or resid 114 through 122 or (resi \ d 123 and (name N or name CA or name C or name O or name CB )) or resid 124 thro \ ugh 133 or (resid 134 and (name N or name CA or name C or name O or name CB )) o \ r resid 135 through 149 or resid 205 through 207 or (resid 208 and (name N or na \ me CA or name C or name O or name CB )) or resid 209 through 215 or (resid 216 a \ nd (name N or name CA or name C or name O or name CB )) or resid 217 through 232 \ or (resid 233 and (name N or name CA or name C or name O or name CB )) or resid \ 234 through 242 or resid 244 through 247 or (resid 248 and (name N or name CA o \ r name C or name O or name CB or name CG1 or name CG2)) or resid 249 through 262 \ or (resid 263 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE )) or resid 264 through 266 or resid 268 through 302 or (r \ esid 303 and (name N or name CA or name C or name O or name CB or name CG or nam \ e SD )) or resid 304 through 330 or (resid 331 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE )) or resid 332 through 34 \ 7 or (resid 348 and (name N or name CA or name C or name O or name CB )) or resi \ d 349 through 351 or (resid 352 and (name N or name CA or name C or name O or na \ me CB )) or resid 353 through 367 or (resid 368 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 369 through 410 or (resid 411 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD1 or name \ CD2 or name CE1 or name CE2 or name CZ )) or resid 412 through 473 or (resid 474 \ and (name N or name CA or name C or name O or name CB )) or resid 475 through 4 \ 84 or (resid 485 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name CE )) or resid 486 through 493 or (resid 494 through 495 an \ d (name N or name CA or name C or name O or name CB )) or resid 496 through 497 \ or (resid 498 and (name N or name CA or name C or name O or name CB )) or resid \ 499 through 506 or (resid 507 and (name N or name CA or name C or name O or name \ CB or name CG1 or name CG2)) or resid 601)) selection = (chain 'I' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB or name CG or name CD )) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG )) or resid 4 through 7 or (resid 8 and (name N \ or name CA or name C or name O or name CB )) or resid 9 through 34 or (resid 35 \ and (name N or name CA or name C or name O or name CB or name CG or name CD )) o \ r resid 36 through 40 or (resid 41 and (name N or name CA or name C or name O or \ name CB )) or resid 42 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB )) or resid 49 through 50 or (resid 51 and (name N or name \ CA or name C or name O or name CB )) or (resid 52 and (name N or name CA or nam \ e C or name O or name CB or name CG1 or name CG2)) or resid 53 through 57 or (re \ sid 58 and (name N or name CA or name C or name O or name CB )) or (resid 59 and \ (name N or name CA or name C or name O or name CB or name CG or name CD )) or r \ esid 60 through 61 or (resid 62 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name CE )) or resid 63 through 67 or (resid 68 an \ d (name N or name CA or name C or name O or name CB or name CG )) or resid 69 th \ rough 71 or (resid 72 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD or name NE or name CZ )) or resid 73 through 84 or (resid 85 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me CE )) or resid 86 through 100 or (resid 101 through 102 and (name N or name C \ A or name C or name O or name CB )) or resid 103 or (resid 104 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name \ CE1 or name CE2 or name CZ )) or resid 105 or (resid 106 and (name N or name CA \ or name C or name O or name CB )) or (resid 109 through 112 and (name N or name \ CA or name C or name O or name CB )) or (resid 113 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE )) or resid 114 throug \ h 122 or (resid 123 and (name N or name CA or name C or name O or name CB )) or \ resid 124 through 133 or (resid 134 and (name N or name CA or name C or name O o \ r name CB )) or resid 135 through 144 or (resid 145 through 146 and (name N or n \ ame CA or name C or name O or name CB )) or resid 147 or (resid 148 through 149 \ and (name N or name CA or name C or name O or name CB )) or resid 205 through 20 \ 7 or (resid 208 and (name N or name CA or name C or name O or name CB )) or resi \ d 209 through 215 or (resid 216 and (name N or name CA or name C or name O or na \ me CB )) or resid 217 through 232 or (resid 233 and (name N or name CA or name C \ or name O or name CB )) or resid 234 or (resid 235 through 238 and (name N or n \ ame CA or name C or name O or name CB )) or resid 239 through 242 or resid 244 t \ hrough 247 or (resid 248 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2)) or resid 249 through 262 or (resid 263 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name CE )) or res \ id 264 through 266 or resid 268 through 290 or resid 293 through 302 or (resid 3 \ 03 and (name N or name CA or name C or name O or name CB or name CG or name SD ) \ ) or resid 304 through 330 or (resid 331 and (name N or name CA or name C or nam \ e O or name CB or name CG or name CD or name CE )) or resid 332 through 347 or ( \ resid 348 and (name N or name CA or name C or name O or name CB )) or resid 349 \ through 350 or (resid 351 through 352 and (name N or name CA or name C or name O \ or name CB )) or resid 353 through 354 or (resid 355 and (name N or name CA or \ name C or name O or name CB or name CG or name CD )) or (resid 356 and (name N o \ r name CA or name C or name O or name CB )) or resid 357 through 410 or (resid 4 \ 11 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2 or name CE1 or name CE2 or name CZ )) or resid 412 through 473 or (r \ esid 474 and (name N or name CA or name C or name O or name CB )) or resid 475 t \ hrough 484 or (resid 485 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name CE )) or resid 486 through 493 or (resid 494 throug \ h 495 and (name N or name CA or name C or name O or name CB )) or (resid 496 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) or \ (resid 497 through 498 and (name N or name CA or name C or name O or name CB )) \ or resid 499 through 506 or (resid 507 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2)) or resid 601)) } ncs_group { reference = chain 'M' selection = chain 'S' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain 'N' selection = chain 'T' selection = chain 'V' selection = chain 'Y' } 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=0.00 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: 7.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 30.790 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 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 : 0.004 0.057 30687 Z= 0.174 Angle : 0.643 15.950 42345 Z= 0.356 Chirality : 0.046 0.806 4865 Planarity : 0.009 0.483 4793 Dihedral : 19.165 144.580 11474 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.89 % Favored : 90.99 % Rotamer: Outliers : 0.45 % Allowed : 24.75 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.14), residues: 3433 helix: 1.11 (0.16), residues: 1044 sheet: -0.78 (0.21), residues: 692 loop : -2.62 (0.13), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 186 TYR 0.020 0.001 TYR I 37 PHE 0.017 0.001 PHE B 217 TRP 0.021 0.001 TRP F 192 HIS 0.003 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00354 (30687) covalent geometry : angle 0.64303 (42345) hydrogen bonds : bond 0.18038 ( 1159) hydrogen bonds : angle 7.16383 ( 3385) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 207 time to evaluate : 0.745 Fit side-chains REVERT: H 226 GLN cc_start: 0.8274 (mt0) cc_final: 0.7951 (mm-40) REVERT: G 391 SER cc_start: 0.7880 (m) cc_final: 0.7074 (p) outliers start: 8 outliers final: 2 residues processed: 213 average time/residue: 0.1662 time to fit residues: 58.5753 Evaluate side-chains 196 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 194 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain B residue 192 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.0870 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 357 GLN I 468 ASN D 320 HIS B 320 HIS ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 HIS ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 HIS ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.068823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.056364 restraints weight = 85403.818| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.11 r_work: 0.2895 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 30687 Z= 0.244 Angle : 0.657 8.985 42345 Z= 0.353 Chirality : 0.046 0.164 4865 Planarity : 0.006 0.065 4793 Dihedral : 16.059 142.817 5662 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.82 % Favored : 90.15 % Rotamer: Outliers : 3.54 % Allowed : 22.67 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.14), residues: 3433 helix: 1.00 (0.16), residues: 1070 sheet: -0.86 (0.20), residues: 705 loop : -2.60 (0.13), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 189 TYR 0.019 0.002 TYR H 190 PHE 0.019 0.002 PHE H 217 TRP 0.017 0.002 TRP B 192 HIS 0.008 0.001 HIS E 360 Details of bonding type rmsd covalent geometry : bond 0.00574 (30687) covalent geometry : angle 0.65745 (42345) hydrogen bonds : bond 0.05674 ( 1159) hydrogen bonds : angle 5.28194 ( 3385) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 199 time to evaluate : 1.171 Fit side-chains REVERT: H 199 ASP cc_start: 0.7921 (p0) cc_final: 0.7691 (p0) REVERT: H 357 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7053 (mt0) REVERT: I 281 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8552 (mp) REVERT: D 209 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.6663 (mtt90) REVERT: D 219 TRP cc_start: 0.8030 (OUTLIER) cc_final: 0.7732 (m-10) REVERT: B 169 GLU cc_start: 0.7717 (tp30) cc_final: 0.7381 (tp30) REVERT: B 389 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7368 (t0) REVERT: B 408 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8089 (tt) REVERT: B 414 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8275 (ttp) REVERT: C 281 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8614 (mp) REVERT: F 21 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8490 (tp) REVERT: F 186 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.6008 (ptp-170) outliers start: 84 outliers final: 37 residues processed: 266 average time/residue: 0.1950 time to fit residues: 84.6839 Evaluate side-chains 228 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 181 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 357 GLN Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 281 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 299 CYS Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 92 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 122 optimal weight: 0.3980 chunk 155 optimal weight: 0.8980 chunk 335 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 272 optimal weight: 0.5980 chunk 118 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 446 ASN D 163 GLN D 262 GLN B 156 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 ASN G 207 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.070089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.057339 restraints weight = 89232.694| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.26 r_work: 0.2916 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30687 Z= 0.142 Angle : 0.576 10.681 42345 Z= 0.309 Chirality : 0.042 0.147 4865 Planarity : 0.005 0.061 4793 Dihedral : 15.917 141.120 5661 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.34 % Favored : 91.64 % Rotamer: Outliers : 2.60 % Allowed : 23.61 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.14), residues: 3433 helix: 1.28 (0.16), residues: 1066 sheet: -0.72 (0.20), residues: 701 loop : -2.54 (0.13), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 382 TYR 0.017 0.001 TYR F 190 PHE 0.024 0.001 PHE B 187 TRP 0.021 0.001 TRP D 192 HIS 0.004 0.001 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00319 (30687) covalent geometry : angle 0.57621 (42345) hydrogen bonds : bond 0.04646 ( 1159) hydrogen bonds : angle 4.92488 ( 3385) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 198 time to evaluate : 1.169 Fit side-chains REVERT: H 199 ASP cc_start: 0.7831 (p0) cc_final: 0.7605 (p0) REVERT: H 386 ASP cc_start: 0.8473 (m-30) cc_final: 0.8213 (m-30) REVERT: D 209 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6572 (mtt90) REVERT: B 169 GLU cc_start: 0.7807 (tp30) cc_final: 0.7452 (tp30) REVERT: B 262 GLN cc_start: 0.8131 (mt0) cc_final: 0.7868 (mt0) REVERT: B 314 GLN cc_start: 0.8558 (tt0) cc_final: 0.8280 (tt0) REVERT: B 363 LYS cc_start: 0.8375 (tppt) cc_final: 0.8158 (ttmm) REVERT: B 389 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7459 (t0) REVERT: B 408 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8043 (tt) REVERT: F 186 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.5945 (ptp-170) REVERT: F 287 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7106 (mtm) outliers start: 61 outliers final: 30 residues processed: 244 average time/residue: 0.1855 time to fit residues: 75.4817 Evaluate side-chains 220 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 156 GLN Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 470 CYS Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 274 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 230 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 chunk 304 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 446 ASN D 358 HIS B 156 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 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 = 0.068311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.055756 restraints weight = 90177.296| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.17 r_work: 0.2878 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 30687 Z= 0.206 Angle : 0.618 10.465 42345 Z= 0.329 Chirality : 0.044 0.152 4865 Planarity : 0.005 0.060 4793 Dihedral : 15.887 139.627 5659 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.62 % Favored : 90.35 % Rotamer: Outliers : 4.15 % Allowed : 22.71 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.14), residues: 3433 helix: 1.23 (0.16), residues: 1069 sheet: -0.75 (0.20), residues: 702 loop : -2.54 (0.13), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 382 TYR 0.021 0.001 TYR F 190 PHE 0.030 0.002 PHE B 187 TRP 0.017 0.001 TRP D 192 HIS 0.008 0.001 HIS E 360 Details of bonding type rmsd covalent geometry : bond 0.00482 (30687) covalent geometry : angle 0.61844 (42345) hydrogen bonds : bond 0.05264 ( 1159) hydrogen bonds : angle 4.88847 ( 3385) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 193 time to evaluate : 1.045 Fit side-chains REVERT: H 199 ASP cc_start: 0.7942 (p0) cc_final: 0.7666 (p0) REVERT: D 179 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8817 (mt) REVERT: D 209 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6627 (mtt90) REVERT: D 287 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8105 (mtt) REVERT: B 169 GLU cc_start: 0.7850 (tp30) cc_final: 0.7487 (tp30) REVERT: B 221 TYR cc_start: 0.5676 (t80) cc_final: 0.4499 (t80) REVERT: B 240 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7301 (tpp80) REVERT: B 297 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8696 (tmtt) REVERT: B 363 LYS cc_start: 0.8440 (tppt) cc_final: 0.8233 (ttmm) REVERT: B 389 ASN cc_start: 0.7806 (OUTLIER) cc_final: 0.7449 (t0) REVERT: B 408 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8100 (tt) REVERT: C 3 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7999 (tp30) REVERT: C 281 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8612 (mp) REVERT: C 414 ASP cc_start: 0.8716 (t0) cc_final: 0.8489 (t0) REVERT: F 21 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8498 (tp) REVERT: F 186 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.6037 (ptp-170) REVERT: F 287 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7188 (mtm) outliers start: 98 outliers final: 61 residues processed: 268 average time/residue: 0.1879 time to fit residues: 84.1467 Evaluate side-chains 255 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 182 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 156 GLN Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 435 MET Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 90 ASN Chi-restraints excluded: chain E residue 91 ILE Chi-restraints excluded: chain E residue 380 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 470 CYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 299 CYS Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 264 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 344 optimal weight: 0.9980 chunk 157 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 315 optimal weight: 0.9990 chunk 268 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 357 GLN E 446 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 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 = 0.3279 r_free = 0.3279 target = 0.069175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.056324 restraints weight = 101455.649| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.33 r_work: 0.2889 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30687 Z= 0.152 Angle : 0.581 10.903 42345 Z= 0.310 Chirality : 0.042 0.146 4865 Planarity : 0.005 0.059 4793 Dihedral : 15.847 139.482 5659 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.80 % Favored : 91.17 % Rotamer: Outliers : 3.87 % Allowed : 23.20 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.22 (0.14), residues: 3433 helix: 1.41 (0.16), residues: 1070 sheet: -0.68 (0.20), residues: 702 loop : -2.49 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 382 TYR 0.017 0.001 TYR F 190 PHE 0.027 0.001 PHE B 187 TRP 0.020 0.001 TRP D 192 HIS 0.004 0.001 HIS E 360 Details of bonding type rmsd covalent geometry : bond 0.00347 (30687) covalent geometry : angle 0.58116 (42345) hydrogen bonds : bond 0.04603 ( 1159) hydrogen bonds : angle 4.72714 ( 3385) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 189 time to evaluate : 1.187 Fit side-chains REVERT: H 199 ASP cc_start: 0.7937 (p0) cc_final: 0.7646 (p0) REVERT: I 222 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.7909 (tp40) REVERT: D 64 SER cc_start: 0.9352 (OUTLIER) cc_final: 0.9059 (p) REVERT: D 179 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8811 (mt) REVERT: D 194 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8213 (tt) REVERT: D 209 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6606 (mtt90) REVERT: B 169 GLU cc_start: 0.7914 (tp30) cc_final: 0.7515 (tp30) REVERT: B 217 PHE cc_start: 0.7965 (t80) cc_final: 0.7720 (m-80) REVERT: B 221 TYR cc_start: 0.5606 (t80) cc_final: 0.4530 (t80) REVERT: B 240 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7074 (tpp80) REVERT: B 262 GLN cc_start: 0.8205 (mt0) cc_final: 0.7966 (mt0) REVERT: B 297 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8694 (tmtt) REVERT: B 389 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7350 (t0) REVERT: B 408 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8060 (tt) REVERT: C 281 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8631 (mp) REVERT: C 414 ASP cc_start: 0.8783 (t0) cc_final: 0.8539 (t0) REVERT: F 186 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.5991 (ptp-170) REVERT: F 277 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8208 (mtm) REVERT: F 287 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7129 (mtm) outliers start: 91 outliers final: 53 residues processed: 258 average time/residue: 0.1856 time to fit residues: 80.1194 Evaluate side-chains 246 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 180 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 156 GLN Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 470 CYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 40 ASP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 82 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 246 optimal weight: 0.0170 chunk 312 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 344 optimal weight: 3.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 446 ASN D 320 HIS ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 320 HIS ** F 370 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 = 0.3249 r_free = 0.3249 target = 0.067911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.055013 restraints weight = 105977.453| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.38 r_work: 0.2854 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 30687 Z= 0.211 Angle : 0.617 11.450 42345 Z= 0.328 Chirality : 0.044 0.150 4865 Planarity : 0.005 0.058 4793 Dihedral : 15.900 139.282 5659 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 4.19 % Allowed : 22.91 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.14), residues: 3433 helix: 1.37 (0.16), residues: 1069 sheet: -0.71 (0.20), residues: 714 loop : -2.48 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 382 TYR 0.021 0.001 TYR D 259 PHE 0.020 0.002 PHE B 187 TRP 0.018 0.001 TRP D 192 HIS 0.008 0.001 HIS E 360 Details of bonding type rmsd covalent geometry : bond 0.00496 (30687) covalent geometry : angle 0.61675 (42345) hydrogen bonds : bond 0.05191 ( 1159) hydrogen bonds : angle 4.79039 ( 3385) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 189 time to evaluate : 1.223 Fit side-chains REVERT: H 199 ASP cc_start: 0.8009 (p0) cc_final: 0.7736 (p0) REVERT: H 226 GLN cc_start: 0.8476 (mt0) cc_final: 0.8272 (mm-40) REVERT: I 222 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.7895 (tp40) REVERT: I 460 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8480 (mp) REVERT: D 64 SER cc_start: 0.9351 (OUTLIER) cc_final: 0.9086 (p) REVERT: D 179 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8832 (mt) REVERT: D 200 VAL cc_start: 0.7907 (t) cc_final: 0.7665 (t) REVERT: D 209 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6713 (mtt90) REVERT: D 413 LYS cc_start: 0.8861 (mtpp) cc_final: 0.8508 (mttm) REVERT: B 169 GLU cc_start: 0.7997 (tp30) cc_final: 0.7567 (tp30) REVERT: B 221 TYR cc_start: 0.5655 (t80) cc_final: 0.4580 (t80) REVERT: B 240 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7144 (tpp80) REVERT: B 297 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8719 (tmtt) REVERT: B 408 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8084 (tt) REVERT: C 3 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8158 (tp30) REVERT: C 281 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8631 (mp) REVERT: C 414 ASP cc_start: 0.8800 (t0) cc_final: 0.8567 (t0) REVERT: F 21 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8517 (tp) REVERT: F 158 PHE cc_start: 0.6458 (m-10) cc_final: 0.6251 (m-10) REVERT: F 186 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6117 (ptp-170) REVERT: F 287 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7204 (mtm) outliers start: 99 outliers final: 66 residues processed: 270 average time/residue: 0.1828 time to fit residues: 83.1212 Evaluate side-chains 259 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 180 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 156 GLN Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 313 LYS Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 380 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 470 CYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 413 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 3 optimal weight: 0.0870 chunk 18 optimal weight: 0.9980 chunk 344 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 333 optimal weight: 0.2980 chunk 349 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 446 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.070005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.057554 restraints weight = 84276.714| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.11 r_work: 0.2929 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30687 Z= 0.125 Angle : 0.560 11.559 42345 Z= 0.299 Chirality : 0.041 0.150 4865 Planarity : 0.004 0.058 4793 Dihedral : 15.809 140.150 5659 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 3.54 % Allowed : 23.85 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.14), residues: 3433 helix: 1.69 (0.16), residues: 1066 sheet: -0.60 (0.20), residues: 692 loop : -2.40 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 382 TYR 0.013 0.001 TYR F 190 PHE 0.014 0.001 PHE B 217 TRP 0.022 0.001 TRP D 192 HIS 0.004 0.001 HIS I 207 Details of bonding type rmsd covalent geometry : bond 0.00276 (30687) covalent geometry : angle 0.56014 (42345) hydrogen bonds : bond 0.04048 ( 1159) hydrogen bonds : angle 4.54214 ( 3385) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 194 time to evaluate : 1.163 Fit side-chains REVERT: H 199 ASP cc_start: 0.7906 (p0) cc_final: 0.7618 (p0) REVERT: H 309 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8276 (mtpp) REVERT: H 329 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8902 (mp) REVERT: I 222 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.7896 (tp40) REVERT: I 413 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8758 (m) REVERT: D 64 SER cc_start: 0.9350 (OUTLIER) cc_final: 0.9107 (p) REVERT: D 179 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8770 (mt) REVERT: D 209 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.6539 (mtt90) REVERT: D 290 THR cc_start: 0.8800 (t) cc_final: 0.8531 (m) REVERT: D 399 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7671 (mt-10) REVERT: D 413 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8554 (mttp) REVERT: B 169 GLU cc_start: 0.7886 (tp30) cc_final: 0.7508 (tp30) REVERT: B 221 TYR cc_start: 0.5710 (t80) cc_final: 0.4602 (t80) REVERT: B 240 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7104 (tpp80) REVERT: B 297 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8586 (tmtt) REVERT: B 389 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7580 (t0) REVERT: B 408 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7941 (tt) REVERT: C 3 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7982 (tp30) REVERT: C 123 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8186 (p0) REVERT: C 414 ASP cc_start: 0.8742 (t0) cc_final: 0.8507 (t0) REVERT: F 181 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8218 (m-10) REVERT: F 186 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.6114 (ptp-170) REVERT: F 277 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8029 (mtm) REVERT: F 287 MET cc_start: 0.7347 (mtp) cc_final: 0.7072 (mtm) REVERT: G 222 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8000 (tp40) REVERT: G 391 SER cc_start: 0.8039 (t) cc_final: 0.7355 (p) outliers start: 83 outliers final: 47 residues processed: 264 average time/residue: 0.1885 time to fit residues: 82.8271 Evaluate side-chains 248 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 313 LYS Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 380 ASN Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 470 CYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 86 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 304 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 238 optimal weight: 0.7980 chunk 313 optimal weight: 0.8980 chunk 301 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 446 ASN B 156 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 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 = 0.3279 r_free = 0.3279 target = 0.069212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.056201 restraints weight = 104687.504| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.46 r_work: 0.2881 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30687 Z= 0.157 Angle : 0.571 11.548 42345 Z= 0.303 Chirality : 0.042 0.148 4865 Planarity : 0.004 0.058 4793 Dihedral : 15.772 138.571 5659 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 3.50 % Allowed : 23.65 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.14), residues: 3433 helix: 1.71 (0.16), residues: 1067 sheet: -0.62 (0.20), residues: 697 loop : -2.38 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 382 TYR 0.014 0.001 TYR F 190 PHE 0.022 0.001 PHE B 187 TRP 0.022 0.001 TRP D 192 HIS 0.005 0.001 HIS E 360 Details of bonding type rmsd covalent geometry : bond 0.00361 (30687) covalent geometry : angle 0.57137 (42345) hydrogen bonds : bond 0.04402 ( 1159) hydrogen bonds : angle 4.56630 ( 3385) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 187 time to evaluate : 1.180 Fit side-chains REVERT: H 199 ASP cc_start: 0.7905 (p0) cc_final: 0.7627 (p0) REVERT: H 309 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8203 (mtpp) REVERT: I 222 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.7773 (tp40) REVERT: I 413 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8707 (m) REVERT: I 460 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8298 (mp) REVERT: D 64 SER cc_start: 0.9332 (OUTLIER) cc_final: 0.9064 (p) REVERT: D 179 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8752 (mt) REVERT: D 200 VAL cc_start: 0.7828 (t) cc_final: 0.7569 (t) REVERT: D 209 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.6542 (mtt90) REVERT: D 290 THR cc_start: 0.8762 (t) cc_final: 0.8482 (m) REVERT: D 413 LYS cc_start: 0.8752 (mtpp) cc_final: 0.8506 (mttp) REVERT: B 169 GLU cc_start: 0.7730 (tp30) cc_final: 0.7345 (tp30) REVERT: B 205 PHE cc_start: 0.8006 (m-80) cc_final: 0.7781 (m-80) REVERT: B 240 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7078 (tpp80) REVERT: B 287 MET cc_start: 0.8767 (mmm) cc_final: 0.8509 (mtp) REVERT: B 297 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8632 (tmtt) REVERT: B 389 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7373 (t0) REVERT: B 408 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7858 (tt) REVERT: C 3 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: C 123 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8098 (p0) REVERT: C 414 ASP cc_start: 0.8569 (t0) cc_final: 0.8333 (t0) REVERT: F 181 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.8175 (m-10) REVERT: F 186 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6116 (ptp-170) REVERT: F 277 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7901 (mtm) REVERT: F 287 MET cc_start: 0.7340 (mtp) cc_final: 0.7050 (mtm) REVERT: G 222 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7870 (tp40) REVERT: G 391 SER cc_start: 0.7949 (t) cc_final: 0.7256 (p) outliers start: 82 outliers final: 59 residues processed: 253 average time/residue: 0.1876 time to fit residues: 79.2595 Evaluate side-chains 257 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 182 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 156 GLN Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 313 LYS Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 222 GLN Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 435 MET Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 380 ASN Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 219 TRP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 470 CYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 413 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 239 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 293 optimal weight: 0.0870 chunk 266 optimal weight: 0.0370 chunk 240 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 314 optimal weight: 0.5980 chunk 228 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 446 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.070140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.057616 restraints weight = 83017.033| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.16 r_work: 0.2927 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30687 Z= 0.123 Angle : 0.557 11.110 42345 Z= 0.296 Chirality : 0.041 0.150 4865 Planarity : 0.004 0.058 4793 Dihedral : 15.712 139.114 5659 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.42 % Allowed : 24.18 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.14), residues: 3433 helix: 1.83 (0.16), residues: 1069 sheet: -0.56 (0.20), residues: 693 loop : -2.36 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 382 TYR 0.012 0.001 TYR F 190 PHE 0.013 0.001 PHE H 205 TRP 0.023 0.001 TRP D 192 HIS 0.003 0.001 HIS I 207 Details of bonding type rmsd covalent geometry : bond 0.00272 (30687) covalent geometry : angle 0.55652 (42345) hydrogen bonds : bond 0.03982 ( 1159) hydrogen bonds : angle 4.46478 ( 3385) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 192 time to evaluate : 1.476 Fit side-chains revert: symmetry clash REVERT: H 199 ASP cc_start: 0.7872 (p0) cc_final: 0.7595 (p0) REVERT: H 309 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8266 (mtpp) REVERT: H 386 ASP cc_start: 0.8503 (m-30) cc_final: 0.8187 (m-30) REVERT: I 413 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8750 (m) REVERT: I 460 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8381 (mp) REVERT: D 64 SER cc_start: 0.9361 (OUTLIER) cc_final: 0.9131 (p) REVERT: D 209 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.6539 (mtt90) REVERT: D 290 THR cc_start: 0.8793 (t) cc_final: 0.8529 (m) REVERT: D 399 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7626 (mt-10) REVERT: D 413 LYS cc_start: 0.8767 (mtpp) cc_final: 0.8502 (mttp) REVERT: B 169 GLU cc_start: 0.7911 (tp30) cc_final: 0.7526 (tp30) REVERT: B 221 TYR cc_start: 0.5698 (t80) cc_final: 0.5220 (t80) REVERT: B 240 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.7000 (tpp80) REVERT: B 297 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8571 (tmtt) REVERT: B 389 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7601 (t0) REVERT: B 408 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7905 (tt) REVERT: C 3 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7992 (tp30) REVERT: C 123 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8122 (p0) REVERT: C 414 ASP cc_start: 0.8760 (t0) cc_final: 0.8515 (t0) REVERT: F 181 PHE cc_start: 0.8620 (OUTLIER) cc_final: 0.8095 (m-10) REVERT: F 186 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6260 (ptp-170) REVERT: F 287 MET cc_start: 0.7401 (mtp) cc_final: 0.7118 (mtm) REVERT: G 222 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.7986 (tp40) REVERT: G 391 SER cc_start: 0.7975 (t) cc_final: 0.7308 (p) outliers start: 80 outliers final: 57 residues processed: 256 average time/residue: 0.1871 time to fit residues: 80.1929 Evaluate side-chains 258 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 188 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 313 LYS Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 380 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 192 TRP Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 470 CYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 413 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 296 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 324 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 82 optimal weight: 0.0470 chunk 58 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 140 optimal weight: 0.0870 chunk 147 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 230 optimal weight: 1.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 446 ASN B 156 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 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 = 0.3275 r_free = 0.3275 target = 0.069017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.056304 restraints weight = 94630.949| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.25 r_work: 0.2892 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30687 Z= 0.165 Angle : 0.579 11.465 42345 Z= 0.306 Chirality : 0.042 0.149 4865 Planarity : 0.004 0.057 4793 Dihedral : 15.674 138.147 5659 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 3.13 % Allowed : 24.30 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.14), residues: 3433 helix: 1.80 (0.16), residues: 1067 sheet: -0.62 (0.20), residues: 702 loop : -2.33 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 382 TYR 0.017 0.001 TYR D 259 PHE 0.024 0.001 PHE B 187 TRP 0.023 0.001 TRP D 192 HIS 0.005 0.001 HIS E 360 Details of bonding type rmsd covalent geometry : bond 0.00382 (30687) covalent geometry : angle 0.57898 (42345) hydrogen bonds : bond 0.04506 ( 1159) hydrogen bonds : angle 4.54663 ( 3385) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6866 Ramachandran restraints generated. 3433 Oldfield, 0 Emsley, 3433 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 185 time to evaluate : 1.200 Fit side-chains REVERT: H 199 ASP cc_start: 0.7897 (p0) cc_final: 0.7646 (p0) REVERT: H 309 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8336 (mtpp) REVERT: H 329 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8957 (mp) REVERT: H 386 ASP cc_start: 0.8516 (m-30) cc_final: 0.8198 (m-30) REVERT: I 460 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8425 (mp) REVERT: D 64 SER cc_start: 0.9351 (OUTLIER) cc_final: 0.9122 (p) REVERT: D 200 VAL cc_start: 0.7921 (t) cc_final: 0.7672 (t) REVERT: D 209 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6640 (mtt90) REVERT: D 290 THR cc_start: 0.8853 (t) cc_final: 0.8586 (m) REVERT: D 413 LYS cc_start: 0.8816 (mtpp) cc_final: 0.8567 (mttp) REVERT: B 169 GLU cc_start: 0.7929 (tp30) cc_final: 0.7573 (tp30) REVERT: B 205 PHE cc_start: 0.8150 (m-80) cc_final: 0.7878 (m-80) REVERT: B 221 TYR cc_start: 0.5820 (t80) cc_final: 0.5434 (t80) REVERT: B 240 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.7031 (tpp80) REVERT: B 291 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: B 297 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8661 (tptm) REVERT: B 389 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7626 (t0) REVERT: B 408 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8119 (tt) REVERT: C 3 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8014 (tp30) REVERT: C 123 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8145 (p0) REVERT: C 414 ASP cc_start: 0.8780 (t0) cc_final: 0.8548 (t0) REVERT: F 181 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8112 (m-10) REVERT: F 186 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6291 (ptp-170) REVERT: F 277 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8206 (mtm) REVERT: F 287 MET cc_start: 0.7446 (mtp) cc_final: 0.7160 (mtm) REVERT: G 222 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8006 (tp40) REVERT: G 391 SER cc_start: 0.8018 (t) cc_final: 0.7380 (p) outliers start: 73 outliers final: 56 residues processed: 244 average time/residue: 0.1883 time to fit residues: 76.7405 Evaluate side-chains 252 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 181 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 156 GLN Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 311 VAL Chi-restraints excluded: chain H residue 313 LYS Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 418 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 305 LEU Chi-restraints excluded: chain I residue 406 MET Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 47 GLN Chi-restraints excluded: chain E residue 221 THR Chi-restraints excluded: chain E residue 305 LEU Chi-restraints excluded: chain E residue 380 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 87 HIS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 192 TRP Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain B residue 34 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 192 TRP Chi-restraints excluded: chain B residue 240 ARG Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 PHE Chi-restraints excluded: chain B residue 297 LYS Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 470 CYS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 69 ASN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 154 TYR Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 181 PHE Chi-restraints excluded: chain F residue 186 ARG Chi-restraints excluded: chain F residue 261 CYS Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 277 MET Chi-restraints excluded: chain F residue 351 ILE Chi-restraints excluded: chain F residue 359 SER Chi-restraints excluded: chain F residue 395 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 GLN Chi-restraints excluded: chain G residue 305 LEU Chi-restraints excluded: chain G residue 317 VAL Chi-restraints excluded: chain G residue 413 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 217 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 145 optimal weight: 0.0870 chunk 21 optimal weight: 0.0030 chunk 136 optimal weight: 1.9990 chunk 305 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 349 optimal weight: 0.8980 chunk 202 optimal weight: 0.2980 overall best weight: 0.3368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 446 ASN B 156 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 370 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 = 0.3316 r_free = 0.3316 target = 0.070837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.057605 restraints weight = 116669.179| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.55 r_work: 0.2918 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30687 Z= 0.111 Angle : 0.547 11.718 42345 Z= 0.290 Chirality : 0.041 0.150 4865 Planarity : 0.004 0.058 4793 Dihedral : 15.593 139.419 5659 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.81 % Allowed : 24.87 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.14), residues: 3433 helix: 1.97 (0.16), residues: 1068 sheet: -0.50 (0.20), residues: 694 loop : -2.28 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 382 TYR 0.011 0.001 TYR F 190 PHE 0.015 0.001 PHE B 217 TRP 0.025 0.001 TRP D 192 HIS 0.004 0.001 HIS I 207 Details of bonding type rmsd covalent geometry : bond 0.00241 (30687) covalent geometry : angle 0.54708 (42345) hydrogen bonds : bond 0.03723 ( 1159) hydrogen bonds : angle 4.37451 ( 3385) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9393.65 seconds wall clock time: 161 minutes 22.52 seconds (9682.52 seconds total)